Historical Contingency of Host-Microbiome Response to Perturbation

Differential Gene Expression Results

Overview

Setup

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Libraries

# Set seed for reproducibility
set.seed(42)

# Load required libraries for DESeq2 analysis and visualization
library(DESeq2)
library(SummarizedExperiment)
library(ggplot2)
library(pheatmap)
library(RColorBrewer)
library(ggrepel)
library(tidyverse)
library(VennDiagram)
library(gridExtra)
library(BiocParallel)
library(gt)
library(broom)
library(car)
library(emmeans)
library(multcomp)
library(MASS)
library(rstatix)
library(coin)

# Load libraries for enrichment analysis
library(clusterProfiler)
library(org.Dr.eg.db)
library(AnnotationDbi)
library(furrr)

Plotting

# Define treatment order and color palette for plotting (original naming convention)
treatment_order_plot <- c(
  "A- T- P-",  # Control
  "A- T- P+",  # Parasite
  "A+ T- P-",  # Antibiotics
  "A+ T- P+",  # Antibiotics_Parasite
  "A- T+ P-",  # Temperature
  "A- T+ P+",  # Temperature_Parasite
  "A+ T+ P-",  # Antibiotics_Temperature
  "A+ T+ P+"   # Antibiotics_Temperature_Parasite
)

# Custom color palette matching treatment order
treatment_colors <- c(
  "#1B9E77",  # A- T- P- (Control)
  "#D95F02",  # A- T- P+ (Parasite)
  "#7570B3",  # A+ T- P- (Antibiotics)
  "#E7298A",  # A+ T- P+ (Antibiotics_Parasite)
  "#66A61E",  # A- T+ P- (Temperature)
  "#E6AB02",  # A- T+ P+ (Temperature_Parasite)
  "#A6761D",  # A+ T+ P- (Antibiotics_Temperature)
  "#666666"   # A+ T+ P+ (Antibiotics_Temperature_Parasite)
)

# Create named vector for color scale
treatment_color_scale <- setNames(treatment_colors, treatment_order_plot)

# Define treatment order for DESeq2 (keep original DESeq2-compatible names)
treatment_order_deseq <- c(
  "A_minus_T_minus_P_minus",  # Control
  "A_minus_T_minus_P_plus",   # Parasite
  "A_plus_T_minus_P_minus",   # Antibiotics
  "A_plus_T_minus_P_plus",    # Antibiotics_Parasite
  "A_minus_T_plus_P_minus",   # Temperature
  "A_minus_T_plus_P_plus",    # Temperature_Parasite
  "A_plus_T_plus_P_minus",    # Antibiotics_Temperature
  "A_plus_T_plus_P_plus"      # Antibiotics_Temperature_Parasite
)

# Create mapping between DESeq2 names and plotting names
treatment_mapping <- setNames(treatment_order_plot, treatment_order_deseq)

# Mapping from DESeq2 contrast names to plotting-friendly names
contrast_to_plotname <- c(
  "A_minus_T_minus_P_minus_vs_A_minus_T_minus_P_minus" = "A- T- P-",
  "A_minus_T_minus_P_plus_vs_A_minus_T_minus_P_minus" = "A- T- P+",
  "A_plus_T_minus_P_minus_vs_A_minus_T_minus_P_minus" = "A+ T- P-",
  "A_plus_T_minus_P_plus_vs_A_minus_T_minus_P_minus" = "A+ T- P+",
  "A_minus_T_plus_P_minus_vs_A_minus_T_minus_P_minus" = "A- T+ P-",
  "A_minus_T_plus_P_plus_vs_A_minus_T_minus_P_minus" = "A- T+ P+",
  "A_plus_T_plus_P_minus_vs_A_minus_T_minus_P_minus" = "A+ T+ P-",
  "A_plus_T_plus_P_plus_vs_A_minus_T_minus_P_minus" = "A+ T+ P+"
)

Functions

# Function to convert DESeq2 treatment names to plotting names
convert_treatment_names <- function(deseq_names) {
  return(treatment_mapping[deseq_names])
}

# Function to monitor system resources during analysis
monitor_performance <- function() {
  # Get memory usage
  mem_usage <- gc()
  
  # Get CPU usage (if possible)
  cpu_info <- tryCatch({
    if (Sys.info()["sysname"] == "Darwin") {
      # macOS
      cpu_cmd <- "top -l 1 -n 0 | grep 'CPU usage'"
      cpu_output <- system(cpu_cmd, intern = TRUE)
      cpu_output
    } else if (Sys.info()["sysname"] == "Linux") {
      # Linux
      cpu_cmd <- "top -bn1 | grep 'Cpu(s)'"
      cpu_output <- system(cpu_cmd, intern = TRUE)
      cpu_output
    } else {
      "CPU monitoring not available on this system"
    }
  }, error = function(e) {
    "CPU monitoring not available"
  })
  
  cat("=== Performance Monitor ===\n")
  cat("Memory usage:\n")
  print(mem_usage)
  cat("CPU info:\n")
  cat(cpu_info, "\n")
  cat("Active parallel workers:", bp_param$workers, "\n")
  cat("========================\n")
}

# Function to optimize memory usage
optimize_memory <- function() {
  cat("Optimizing memory usage...\n")
  
  # Force garbage collection
  gc(verbose = FALSE)
  
  # Clear unnecessary objects
  if (exists("temp_objects")) {
    rm(temp_objects)
  }
  
  cat("Memory optimization complete\n")
}

# Function to save DESeq2 results
save_deseq_results <- function(results_list, analysis_name) {
  # Create results directory if it doesn't exist
  results_dir <- here::here("Code", "Analysis", "DiffExpGene", "Saved_Results")
  dir.create(results_dir, recursive = TRUE, showWarnings = FALSE)
  
  # Save the results list
  results_file <- file.path(results_dir, paste0(analysis_name, "_deseq_results.rds"))
  saveRDS(results_list, results_file)
  
  cat("Results saved to:", results_file, "\n")
}

# Function to load DESeq2 results
load_deseq_results <- function(analysis_name) {
  results_dir <- here::here("Code", "Analysis", "DiffExpGene", "Saved_Results")
  results_file <- file.path(results_dir, paste0(analysis_name, "_deseq_results.rds"))
  
  if (file.exists(results_file)) {
    cat("Loading existing results for:", analysis_name, "\n")
    return(readRDS(results_file))
  } else {
    cat("No existing results found for:", analysis_name, "\n")
    return(NULL)
  }
}

# Function to check if results exist
results_exist <- function(analysis_name) {
  results_dir <- here::here("Code", "Analysis", "DiffExpGene", "Saved_Results")
  results_file <- file.path(results_dir, paste0(analysis_name, "_deseq_results.rds"))
  return(file.exists(results_file))
}

# Function to clean up saved results
cleanup_saved_results <- function(analysis_names = NULL) {
  results_dir <- here::here("Code", "Analysis", "DiffExpGene", "Saved_Results")
  
  if (is.null(analysis_names)) {
    # Remove all saved results
    if (dir.exists(results_dir)) {
      unlink(results_dir, recursive = TRUE)
      cat("All saved results removed\n")
    }
  } else {
    # Remove specific analysis results
    for (analysis_name in analysis_names) {
      results_file <- file.path(results_dir, paste0(analysis_name, "_deseq_results.rds"))
      if (file.exists(results_file)) {
        file.remove(results_file)
        cat("Removed saved results for:", analysis_name, "\n")
      }
    }
  }
}

# Function to run DESeq2 analysis for a single comparison
run_deseq_comparison <- function(dds, contrast_name, contrast_vector) {
  cat("Running analysis for:", contrast_name, "\n")
  
  # Set seed for reproducibility within parallel processes
  set.seed(42)
  
  # Optimize DESeq2 settings for speed
  # Use faster estimation method for large datasets
  if (nrow(dds) > 10000) {
    # For large datasets, use faster estimation
    dds_comparison <- DESeq(dds, 
                           parallel = TRUE,
                           fitType = "local",  # Faster than "parametric"
                           betaPrior = FALSE,  # Disable beta prior for speed
                           quiet = FALSE)
  } else {
    # For smaller datasets, use standard settings
    dds_comparison <- DESeq(dds, 
                           parallel = TRUE,
                           quiet = FALSE)
  }
  
  # Get results with optimized settings
  res_comparison <- results(dds_comparison, 
                           contrast = contrast_vector,
                           parallel = TRUE,
                           alpha = 0.05)  # Set significance threshold
  
  # Add gene names if available
  if ("gene_name" %in% names(mcols(dds_comparison))) {
    res_comparison$gene_name <- mcols(dds_comparison)$gene_name
  }
  
  # Clean up memory
  rm(dds_comparison)
  gc()
  
  return(res_comparison)
}

# Function to run all comparisons for a specific analysis with enhanced parallelization
run_analysis_set <- function(analysis_name, analysis_config, force_recompute = FALSE) {
  cat("\n=== Running", analysis_name, "===\n")
  cat("Description:", analysis_config$description, "\n")
  
  # Check if results already exist and force_recompute is FALSE
  if (!force_recompute && results_exist(analysis_name)) {
    cat("Loading existing results for", analysis_name, "\n")
    return(load_deseq_results(analysis_name))
  }
  
  # Create a copy of the dataset for this analysis
  dds_analysis <- dds_filtered
  
  # Update design if needed
  design(dds_analysis) <- analysis_config$design
  
  # Pre-estimate size factors and dispersions for better parallelization
  cat("Pre-estimating size factors and dispersions...\n")
  dds_analysis <- estimateSizeFactors(dds_analysis)
  dds_analysis <- estimateDispersions(dds_analysis)
  
  # Run all contrasts for this analysis
  results_list <- list()
  
  # Use parallel processing for multiple contrasts
  if (length(analysis_config$contrasts) > 1) {
    cat("Running", length(analysis_config$contrasts), "contrasts in parallel...\n")
    
    # Create a function for parallel execution
    run_single_contrast <- function(contrast_info) {
      contrast_name <- contrast_info$name
      contrast_vector <- contrast_info$vector
      
      # Check if both treatment levels exist in the data
      if (all(contrast_vector[2:3] %in% levels(colData(dds_analysis)$Treatment))) {
        return(list(name = contrast_name, result = run_deseq_comparison(dds_analysis, contrast_name, contrast_vector)))
      } else {
        cat("Warning: Contrast", contrast_name, "skipped - treatment levels not found in data\n")
        return(list(name = contrast_name, result = NULL))
      }
    }
    
    # Prepare contrast information for parallel processing
    contrast_info_list <- lapply(names(analysis_config$contrasts), function(name) {
      list(name = name, vector = analysis_config$contrasts[[name]])
    })
    
    # Run contrasts in parallel
    parallel_results <- BiocParallel::bplapply(contrast_info_list, run_single_contrast)
    
    # Organize results
    for (result in parallel_results) {
      if (!is.null(result$result)) {
        results_list[[result$name]] <- result$result
      }
    }
    
  } else {
    # For single contrast, run directly
    for (contrast_name in names(analysis_config$contrasts)) {
      contrast_vector <- analysis_config$contrasts[[contrast_name]]
      
      # Check if both treatment levels exist in the data
      if (all(contrast_vector[2:3] %in% levels(colData(dds_analysis)$Treatment))) {
        results_list[[contrast_name]] <- run_deseq_comparison(dds_analysis, contrast_name, contrast_vector)
      } else {
        cat("Warning: Contrast", contrast_name, "skipped - treatment levels not found in data\n")
      }
    }
  }
  
  # Save the results
  save_deseq_results(results_list, analysis_name)
  
  # Clean up memory
  rm(dds_analysis)
  gc()
  
  return(results_list)
}

# Function to format p-values for gt tables
fmt_pvalues <- function(gt_tbl, columns, threshold = 0.001, decimals = 3) {
  gt_tbl |>
    gt::fmt_number(columns = all_of(columns), decimals = decimals) |>
    gt::fmt(
      columns = all_of(columns),
      rows = Reduce(`|`, lapply(columns, function(col) gt_tbl$`_data`[[col]] < threshold)),
      fns = function(x) rep(paste0("<", threshold), length(x))
    )
}

# Function to save results for each analysis
save_analysis_results <- function(analysis_name, results_list) {
  cat("Saving results for:", analysis_name, "\n")
  
  # Create subdirectory for this analysis
  analysis_dir <- file.path(output_dir, analysis_name)
  dir.create(analysis_dir, recursive = TRUE, showWarnings = FALSE)
  
  # Save each contrast result
  for (contrast_name in names(results_list)) {
    res <- results_list[[contrast_name]]
    
    # Convert to data frame
    res_df <- as.data.frame(res) %>% rownames_to_column(var = "gene")
    
    # Add gene names if available
    if ("gene_name" %in% names(res_df)) {
      res_df <- res_df %>% 
        dplyr::select(gene_name, everything()) %>%
        dplyr::rename(gene = gene_name)
    }
    
    # Save full results
    full_filename <- file.path(analysis_dir, paste0(contrast_name, "_full_results.tsv"))
    write_tsv(res_df, full_filename)
    
    # Save significant results (padj < 0.05)
    sig_df <- res_df %>% 
      dplyr::filter(padj < 0.05) %>%
      dplyr::arrange(padj)
    
    if (nrow(sig_df) > 0) {
      sig_filename <- file.path(analysis_dir, paste0(contrast_name, "_significant_results.tsv"))
      write_tsv(sig_df, sig_filename)
      
      # Create summary table
      summary_table <- data.frame(
        Contrast = contrast_name,
        Total_Genes = nrow(res_df),
        Significant_Genes = nrow(sig_df),
        Upregulated = sum(sig_df$log2FoldChange > 0, na.rm = TRUE),
        Downregulated = sum(sig_df$log2FoldChange < 0, na.rm = TRUE),
        stringsAsFactors = FALSE
      )
      
      # Save summary
      summary_filename <- file.path(analysis_dir, paste0(contrast_name, "_summary.tsv"))
      write_tsv(summary_table, summary_filename)
    }
  }
  
  # Create combined summary for the analysis
  all_summaries <- list()
  for (contrast_name in names(results_list)) {
    res <- results_list[[contrast_name]]
    res_df <- as.data.frame(res)
    sig_df <- res_df %>% dplyr::filter(padj < 0.05)
    
    all_summaries[[contrast_name]] <- data.frame(
      Contrast = contrast_name,
      Total_Genes = nrow(res_df),
      Significant_Genes = nrow(sig_df),
      Upregulated = sum(sig_df$log2FoldChange > 0, na.rm = TRUE),
      Downregulated = sum(sig_df$log2FoldChange < 0, na.rm = TRUE),
      stringsAsFactors = FALSE
    )
  }
  
  combined_summary <- bind_rows(all_summaries)
  combined_filename <- file.path(analysis_dir, paste0(analysis_name, "_combined_summary.tsv"))
  write_tsv(combined_summary, combined_filename)
  
  # Display summary table
  cat("\nSummary for", analysis_name, ":\n")
  print(combined_summary %>% gt::gt())
}

# Function to convert gene IDs to Entrez IDs for enrichment analysis
get_entrez_ids <- function(deg_df) {
  # Set seed for reproducibility
  set.seed(42)
  
  # Use org.Dr.eg.db to map gene symbols to Entrez IDs
  gene_ids <- deg_df$gene
  
  # Create a mapping dataframe
  entrez_map <- AnnotationDbi::mapIds(
    org.Dr.eg.db,
    keys = gene_ids,
    column = "ENTREZID",
    keytype = "SYMBOL",
    multiVals = "first"
  ) %>%
    tibble::enframe(name = "gene", value = "entrezgene_id") %>%
    dplyr::filter(!is.na(entrezgene_id))
  
  # Join with original data to keep all information
  result <- deg_df %>%
    dplyr::left_join(entrez_map, by = "gene") %>%
    dplyr::filter(!is.na(entrezgene_id)) %>%
    dplyr::distinct(entrezgene_id, .keep_all = TRUE)
  
  return(result)
}

# Function to perform GO enrichment analysis
perform_go_enrichment <- function(entrez_df, contrast_name) {
  # Set seed for reproducibility
  set.seed(42)
  
  cat("Performing GO enrichment for:", contrast_name, "\n")
  cat("Number of genes:", nrow(entrez_df), "\n")
  
  # Perform GO enrichment
  go_results <- clusterProfiler::enrichGO(
    gene = entrez_df$entrezgene_id,
    OrgDb = org.Dr.eg.db,
    keyType = "ENTREZID",
    ont = "BP",  # Biological Process
    pAdjustMethod = "BH",
    pvalueCutoff = 0.1,
    readable = TRUE
  ) %>%
    as.data.frame() %>%
    dplyr::select(Description, p.adjust, Count, geneID) %>%
    dplyr::mutate(log_padj = -log10(p.adjust))
  
  # Create a mapping of gene symbols to Entrez IDs
  symbol_to_entrez <- AnnotationDbi::mapIds(
    org.Dr.eg.db,
    keys = entrez_df$entrezgene_id,
    column = "SYMBOL",
    keytype = "ENTREZID",
    multiVals = "first"
  ) %>%
    tibble::enframe(name = "entrezgene_id", value = "SYMBOL") %>%
    dplyr::filter(!is.na(SYMBOL))
  
  # Create a mapping of gene IDs to log2FoldChange
  gene_fc_map <- entrez_df %>%
    dplyr::select(entrezgene_id, log2FoldChange) %>%
    dplyr::left_join(symbol_to_entrez, by = "entrezgene_id") %>%
    dplyr::select(SYMBOL, log2FoldChange) %>%
    dplyr::filter(!is.na(SYMBOL))
  
  # Split the geneID column and create a long format dataframe
  go_results_long <- go_results %>%
    tidyr::separate_rows(geneID, sep = "/") %>%
    # Join with the fold change data using gene symbols
    dplyr::left_join(gene_fc_map, by = c("geneID" = "SYMBOL"))
  
  # Group back by GO term and calculate summary statistics
  go_results_summary <- go_results_long %>%
    dplyr::group_by(Description, p.adjust, Count, log_padj) %>%
    dplyr::summarise(
      mean_log2FC = mean(log2FoldChange, na.rm = TRUE),
      n_up = sum(log2FoldChange > 0, na.rm = TRUE),
      n_down = sum(log2FoldChange < 0, na.rm = TRUE),
      gene_list = list(geneID),
      fc_list = list(log2FoldChange),
      .groups = "drop"
    )
  
  return(go_results_summary)
}

# Function to perform KEGG enrichment analysis
perform_kegg_enrichment <- function(entrez_df, contrast_name) {
  # Set seed for reproducibility
  set.seed(42)
  
  cat("Performing KEGG enrichment for:", contrast_name, "\n")
  cat("Number of genes:", nrow(entrez_df), "\n")
  
  # Perform KEGG enrichment
  kegg_results <- clusterProfiler::enrichKEGG(
    gene = entrez_df$entrezgene_id,
    organism = 'dre',  # Danio rerio
    keyType = 'ncbi-geneid',
    pvalueCutoff = 0.1,
    pAdjustMethod = "BH"
  ) %>%
    as.data.frame() %>%
    dplyr::select(Description, p.adjust, Count, geneID) %>%
    dplyr::mutate(log_padj = -log10(p.adjust))
  
  # Create a mapping of gene IDs to log2FoldChange
  gene_fc_map <- entrez_df %>%
    dplyr::select(entrezgene_id, log2FoldChange) %>%
    dplyr::mutate(entrezgene_id = as.character(entrezgene_id))
  
  # Split the geneID column and create a long format dataframe
  kegg_results_long <- kegg_results %>%
    tidyr::separate_rows(geneID, sep = "/") %>%
    # Convert geneID to character for joining
    dplyr::mutate(geneID = as.character(geneID)) %>%
    # Join with the fold change data
    dplyr::left_join(gene_fc_map, by = c("geneID" = "entrezgene_id"))
  
  # Group back by KEGG pathway and calculate summary statistics
  kegg_results_summary <- kegg_results_long %>%
    dplyr::group_by(Description, p.adjust, Count, log_padj) %>%
    dplyr::summarise(
      mean_log2FC = mean(log2FoldChange, na.rm = TRUE),
      n_up = sum(log2FoldChange > 0, na.rm = TRUE),
      n_down = sum(log2FoldChange < 0, na.rm = TRUE),
      gene_list = list(geneID),
      fc_list = list(log2FoldChange),
      .groups = "drop"
    )
  
  return(kegg_results_summary)
}

# Function to prepare data for enrichment heatmaps
prepare_enrichment_heatmap <- function(enrichment_results, top_n = 15) {
  # Get top terms from each contrast
  top_terms <- enrichment_results %>%
    purrr::map(~ dplyr::slice_max(.x, order_by = log_padj, n = top_n)) %>%
    purrr::map(~ dplyr::pull(.x, Description)) %>%
    unlist() %>%
    unique()
  
  # Create matrix for heatmap
  heatmap_data <- enrichment_results %>%
    purrr::map_dfr(~ dplyr::filter(.x, Description %in% top_terms), .id = "contrast") %>%
    # Convert contrast names to readable format
    dplyr::mutate(contrast = purrr::map_chr(contrast, convert_contrast_names)) %>%
    tidyr::pivot_wider(
      id_cols = Description,
      names_from = contrast,
      values_from = log_padj,
      values_fill = 0
    ) %>%
    tibble::column_to_rownames("Description") %>%
    as.matrix()
  
  return(heatmap_data)
}

# Function to prepare data for regulation heatmaps
prepare_regulation_heatmap <- function(enrichment_results, direction = "up", top_n = 20) {
  # Combine all results
  all_results <- purrr::map_dfr(enrichment_results, ~.x, .id = "contrast")
  
  # Convert contrast names to readable format
  all_results <- all_results %>%
    dplyr::mutate(contrast = purrr::map_chr(contrast, convert_contrast_names))
  
  # Filter for terms with significant regulation in the specified direction
  filtered_terms <- all_results %>%
    dplyr::filter(
      if(direction == "up") {
        n_up > n_down
      } else {
        n_down > n_up
      }
    ) %>%
    dplyr::group_by(Description) %>%
    dplyr::summarise(
      total_terms = n(),
      mean_fc = mean(mean_log2FC, na.rm = TRUE),
      .groups = "drop"
    ) %>%
    dplyr::arrange(desc(total_terms)) %>%
    dplyr::slice_head(n = top_n)
  
  # Create heatmap data
  heatmap_data <- all_results %>%
    dplyr::filter(Description %in% filtered_terms$Description) %>%
    dplyr::select(contrast, Description, mean_log2FC) %>%
    tidyr::pivot_wider(
      names_from = contrast,
      values_from = mean_log2FC,
      values_fill = 0
    ) %>%
    tibble::column_to_rownames("Description")
  
  # Set color scheme based on direction
  if(direction == "up") {
    color_scheme <- colorRampPalette(c("white", "red"))(100)
    # For up-regulated, we want to show the magnitude of positive changes
    heatmap_data[heatmap_data < 0] <- 0
  } else {
    color_scheme <- colorRampPalette(c("white", "blue"))(100)
    # For down-regulated, we want to show the magnitude of negative changes
    heatmap_data[heatmap_data > 0] <- 0
    # Make negative values positive for visualization
    heatmap_data <- abs(heatmap_data)
  }
  
  return(list(heatmap_data = heatmap_data, color_scheme = color_scheme))
}

# Function to run enrichment analysis for a specific analysis
run_enrichment_analysis <- function(analysis_name, results_list) {
  cat("\n=== Running Enrichment Analysis for:", analysis_name, "===\n")
  
  # Convert results to tidy format and filter significant genes
  contrast_tibbles <- purrr::map(results_list, ~
    as.data.frame(.) %>%
      tibble::rownames_to_column("gene") %>%
      dplyr::filter(
        padj < 0.05, 
        abs(log2FoldChange) > 1,
        !gene %in% genes_to_exclude  # Filter out excluded genes
      ) %>%
      dplyr::select(gene, log2FoldChange, padj)
  )
  
  # Convert to Entrez IDs
  entrez_by_contrast <- purrr::map(contrast_tibbles, get_entrez_ids)
  
  # Run GO enrichment
  cat("Running GO enrichment...\n")
  go_by_contrast <- purrr::map2(entrez_by_contrast, names(entrez_by_contrast), 
                               perform_go_enrichment)
  names(go_by_contrast) <- names(entrez_by_contrast)
  
  # Run KEGG enrichment
  cat("Running KEGG enrichment...\n")
  kegg_by_contrast <- purrr::map2(entrez_by_contrast, names(entrez_by_contrast), 
                                 perform_kegg_enrichment)
  names(kegg_by_contrast) <- names(entrez_by_contrast)
  
  return(list(
    go_results = go_by_contrast,
    kegg_results = kegg_by_contrast,
    entrez_data = entrez_by_contrast
  ))
}

# Function to convert DESeq2 contrast names to readable format
convert_contrast_names <- function(contrast_name) {
  # Define mapping for common contrast patterns
  contrast_mapping <- c(
    "A_minus_T_minus_P_plus_vs_A_minus_T_minus_P_minus" = "A- T- P+ vs A- T- P-",
    "A_plus_T_minus_P_minus_vs_A_minus_T_minus_P_minus" = "A+ T- P- vs A- T- P-",
    "A_plus_T_minus_P_plus_vs_A_minus_T_minus_P_minus" = "A+ T- P+ vs A- T- P-",
    "A_minus_T_plus_P_minus_vs_A_minus_T_minus_P_minus" = "A- T+ P- vs A- T- P-",
    "A_minus_T_plus_P_plus_vs_A_minus_T_minus_P_minus" = "A- T+ P+ vs A- T- P-",
    "A_plus_T_plus_P_minus_vs_A_minus_T_minus_P_minus" = "A+ T+ P- vs A- T- P-",
    "A_plus_T_plus_P_plus_vs_A_minus_T_minus_P_minus" = "A+ T+ P+ vs A- T- P-",
    "A_plus_T_minus_P_plus_vs_A_minus_T_minus_P_plus" = "A+ T- P+ vs A- T- P+",
    "A_minus_T_plus_P_plus_vs_A_minus_T_minus_P_plus" = "A- T+ P+ vs A- T- P+",
    "A_plus_T_plus_P_plus_vs_A_minus_T_minus_P_plus" = "A+ T+ P+ vs A- T- P+"
  )
  
  # Check if the contrast name is in our mapping
  if (contrast_name %in% names(contrast_mapping)) {
    return(contrast_mapping[contrast_name])
  } else {
    # If not in mapping, try to convert using pattern matching
    # Replace underscores with spaces and convert to readable format
    readable_name <- contrast_name %>%
      stringr::str_replace_all("_minus", "-") %>%
      stringr::str_replace_all("_plus", "+") %>%
      stringr::str_replace_all("_vs_", " vs ") %>%
      stringr::str_replace_all("A", "A") %>%
      stringr::str_replace_all("T", "T") %>%
      stringr::str_replace_all("P", "P")
    
    return(readable_name)
  }
}

# Function to save enrichment results
save_enrichment_results <- function(enrichment_results, analysis_name) {
  cat("Saving enrichment results for:", analysis_name, "\n")
  
  # Create subdirectory for this analysis
  analysis_dir <- file.path(output_dir, analysis_name, "enrichment")
  dir.create(analysis_dir, recursive = TRUE, showWarnings = FALSE)
  
  # Save individual contrast GO results (all terms, not just top)
  for (contrast_name in names(enrichment_results$go_results)) {
    go_res <- enrichment_results$go_results[[contrast_name]]
    if (nrow(go_res) > 0) {
      # Save all GO results for this contrast
      go_filename <- file.path(analysis_dir, paste0(contrast_name, "_GO_enrichment_ALL.tsv"))
      write_tsv(go_res, go_filename)
      
      # Also save top 20 for quick reference
      go_top20 <- go_res %>% dplyr::slice_max(order_by = log_padj, n = 20)
      go_top20_filename <- file.path(analysis_dir, paste0(contrast_name, "_GO_enrichment_TOP20.tsv"))
      write_tsv(go_top20, go_top20_filename)
    }
  }
  
  # Save individual contrast KEGG results (all pathways, not just top)
  for (contrast_name in names(enrichment_results$kegg_results)) {
    kegg_res <- enrichment_results$kegg_results[[contrast_name]]
    if (nrow(kegg_res) > 0) {
      # Save all KEGG results for this contrast
      kegg_filename <- file.path(analysis_dir, paste0(contrast_name, "_KEGG_enrichment_ALL.tsv"))
      write_tsv(kegg_res, kegg_filename)
      
      # Also save top 20 for quick reference
      kegg_top20 <- kegg_res %>% dplyr::slice_max(order_by = log_padj, n = 20)
      kegg_top20_filename <- file.path(analysis_dir, paste0(contrast_name, "_KEGG_enrichment_TOP20.tsv"))
      write_tsv(kegg_top20, kegg_top20_filename)
    }
  }
  
  # Save combined summary (all results across contrasts)
  if (length(enrichment_results$go_results) > 0) {
    go_summary <- purrr::map_dfr(enrichment_results$go_results, ~.x, .id = "contrast")
    go_summary_filename <- file.path(analysis_dir, paste0(analysis_name, "_GO_summary_ALL.tsv"))
    write_tsv(go_summary, go_summary_filename)
    
    # Save top 50 GO terms across all contrasts
    go_top50 <- go_summary %>% 
      dplyr::slice_max(order_by = log_padj, n = 50)
    go_top50_filename <- file.path(analysis_dir, paste0(analysis_name, "_GO_summary_TOP50.tsv"))
    write_tsv(go_top50, go_top50_filename)
  }
  
  if (length(enrichment_results$kegg_results) > 0) {
    kegg_summary <- purrr::map_dfr(enrichment_results$kegg_results, ~.x, .id = "contrast")
    kegg_summary_filename <- file.path(analysis_dir, paste0(analysis_name, "_KEGG_summary_ALL.tsv"))
    write_tsv(kegg_summary, kegg_summary_filename)
    
    # Save top 50 KEGG pathways across all contrasts
    kegg_top50 <- kegg_summary %>% 
      dplyr::slice_max(order_by = log_padj, n = 50)
    kegg_top50_filename <- file.path(analysis_dir, paste0(analysis_name, "_KEGG_summary_TOP50.tsv"))
    write_tsv(kegg_top50, kegg_top50_filename)
  }
  
  # Save significant results only (padj < 0.05)
  if (length(enrichment_results$go_results) > 0) {
    go_significant <- purrr::map_dfr(enrichment_results$go_results, ~.x, .id = "contrast") %>%
      dplyr::filter(p.adjust < 0.05)
    if (nrow(go_significant) > 0) {
      go_sig_filename <- file.path(analysis_dir, paste0(analysis_name, "_GO_significant.tsv"))
      write_tsv(go_significant, go_sig_filename)
    }
  }
  
  if (length(enrichment_results$kegg_results) > 0) {
    kegg_significant <- purrr::map_dfr(enrichment_results$kegg_results, ~.x, .id = "contrast") %>%
      dplyr::filter(p.adjust < 0.05)
    if (nrow(kegg_significant) > 0) {
      kegg_sig_filename <- file.path(analysis_dir, paste0(analysis_name, "_KEGG_significant.tsv"))
      write_tsv(kegg_significant, kegg_sig_filename)
    }
  }
  
  # Create and save a comprehensive summary report
  create_comprehensive_report(enrichment_results, analysis_name, analysis_dir)
  
  cat("Enrichment results saved to:", analysis_dir, "\n")
}

# Function to create comprehensive enrichment report
create_comprehensive_report <- function(enrichment_results, analysis_name, analysis_dir) {
  cat("Creating comprehensive report for:", analysis_name, "\n")
  
  # Initialize report data
  report_data <- list()
  
  # GO analysis summary
  if (length(enrichment_results$go_results) > 0) {
    go_all <- purrr::map_dfr(enrichment_results$go_results, ~.x, .id = "contrast")
    
    report_data$go_summary <- list(
      total_terms = nrow(go_all),
      significant_terms = sum(go_all$p.adjust < 0.05, na.rm = TRUE),
      contrasts_analyzed = length(enrichment_results$go_results),
      top_terms = go_all %>% dplyr::slice_max(order_by = log_padj, n = 10),
      significant_terms_list = go_all %>% dplyr::filter(p.adjust < 0.05) %>% dplyr::arrange(p.adjust)
    )
  }
  
  # KEGG analysis summary
  if (length(enrichment_results$kegg_results) > 0) {
    kegg_all <- purrr::map_dfr(enrichment_results$kegg_results, ~.x, .id = "contrast")
    
    report_data$kegg_summary <- list(
      total_pathways = nrow(kegg_all),
      significant_pathways = sum(kegg_all$p.adjust < 0.05, na.rm = TRUE),
      contrasts_analyzed = length(enrichment_results$kegg_results),
      top_pathways = kegg_all %>% dplyr::slice_max(order_by = log_padj, n = 10),
      significant_pathways_list = kegg_all %>% dplyr::filter(p.adjust < 0.05) %>% dplyr::arrange(p.adjust)
    )
  }
  
  # Save comprehensive report as RDS
  report_filename <- file.path(analysis_dir, paste0(analysis_name, "_comprehensive_report.rds"))
  saveRDS(report_data, report_filename)
  
  # Create and save a text summary
  summary_text <- paste0(
    "=== ENRICHMENT ANALYSIS REPORT ===\n",
    "Analysis: ", analysis_name, "\n",
    "Date: ", format(Sys.time(), "%Y-%m-%d %H:%M:%S"), "\n\n",
    
    "GO ENRICHMENT SUMMARY:\n",
    ifelse(length(enrichment_results$go_results) > 0,
           paste0("  Total terms analyzed: ", report_data$go_summary$total_terms, "\n",
                  "  Significant terms (padj < 0.05): ", report_data$go_summary$significant_terms, "\n",
                  "  Contrasts analyzed: ", report_data$go_summary$contrasts_analyzed, "\n"),
           "  No GO results available\n"),
    "\n",
    
    "KEGG ENRICHMENT SUMMARY:\n",
    ifelse(length(enrichment_results$kegg_results) > 0,
           paste0("  Total pathways analyzed: ", report_data$kegg_summary$total_pathways, "\n",
                  "  Significant pathways (padj < 0.05): ", report_data$kegg_summary$significant_pathways, "\n",
                  "  Contrasts analyzed: ", report_data$kegg_summary$contrasts_analyzed, "\n"),
           "  No KEGG results available\n"),
    "\n",
    
    "FILES SAVED:\n",
    "  - Individual contrast files (ALL and TOP20)\n",
    "  - Combined summary files (ALL and TOP50)\n",
    "  - Significant results only (padj < 0.05)\n",
    "  - Comprehensive report (RDS format)\n",
    "  - This text summary\n"
  )
  
  summary_filename <- file.path(analysis_dir, paste0(analysis_name, "_analysis_summary.txt"))
  writeLines(summary_text, summary_filename)
  
  cat("Comprehensive report saved to:", report_filename, "\n")
  cat("Text summary saved to:", summary_filename, "\n")
}

# Function to create combined enrichment summary across all analyses
create_combined_enrichment_summary <- function(enrichment_results) {
  cat("Creating combined enrichment summary across all analyses...\n")
  
  # Create combined directory
  combined_dir <- file.path(output_dir, "Combined_Enrichment_Results")
  dir.create(combined_dir, recursive = TRUE, showWarnings = FALSE)
  
  # Combine all GO results
  all_go_results <- list()
  all_kegg_results <- list()
  
  for (analysis_name in names(enrichment_results)) {
    if (!is.null(enrichment_results[[analysis_name]]$go_results)) {
      go_data <- purrr::map_dfr(enrichment_results[[analysis_name]]$go_results, ~.x, .id = "contrast") %>%
        dplyr::mutate(analysis = analysis_name)
      all_go_results[[analysis_name]] <- go_data
    }
    
    if (!is.null(enrichment_results[[analysis_name]]$kegg_results)) {
      kegg_data <- purrr::map_dfr(enrichment_results[[analysis_name]]$kegg_results, ~.x, .id = "contrast") %>%
        dplyr::mutate(analysis = analysis_name)
      all_kegg_results[[analysis_name]] <- kegg_data
    }
  }
  
  # Save combined GO results
  if (length(all_go_results) > 0) {
    combined_go <- dplyr::bind_rows(all_go_results) %>%
      dplyr::arrange(analysis, contrast, desc(log_padj))
    
    # Save all GO results
    combined_go_filename <- file.path(combined_dir, "ALL_ANALYSES_GO_enrichment_ALL.tsv")
    write_tsv(combined_go, combined_go_filename)
    
    # Save top 100 GO terms across all analyses
    combined_go_top100 <- combined_go %>% 
      dplyr::slice_max(order_by = log_padj, n = 100)
    combined_go_top100_filename <- file.path(combined_dir, "ALL_ANALYSES_GO_enrichment_TOP100.tsv")
    write_tsv(combined_go_top100, combined_go_top100_filename)
    
    # Save significant GO terms only
    combined_go_sig <- combined_go %>% 
      dplyr::filter(p.adjust < 0.05)
    if (nrow(combined_go_sig) > 0) {
      combined_go_sig_filename <- file.path(combined_dir, "ALL_ANALYSES_GO_enrichment_SIGNIFICANT.tsv")
      write_tsv(combined_go_sig, combined_go_sig_filename)
    }
    
    cat("Combined GO results saved:\n")
    cat("  - All results:", combined_go_filename, "\n")
    cat("  - Top 100:", combined_go_top100_filename, "\n")
    if (nrow(combined_go_sig) > 0) {
      cat("  - Significant only:", combined_go_sig_filename, "\n")
    }
  }
  
  # Save combined KEGG results
  if (length(all_kegg_results) > 0) {
    combined_kegg <- dplyr::bind_rows(all_kegg_results) %>%
      dplyr::arrange(analysis, contrast, desc(log_padj))
    
    # Save all KEGG results
    combined_kegg_filename <- file.path(combined_dir, "ALL_ANALYSES_KEGG_enrichment_ALL.tsv")
    write_tsv(combined_kegg, combined_kegg_filename)
    
    # Save top 100 KEGG pathways across all analyses
    combined_kegg_top100 <- combined_kegg %>% 
      dplyr::slice_max(order_by = log_padj, n = 100)
    combined_kegg_top100_filename <- file.path(combined_dir, "ALL_ANALYSES_KEGG_enrichment_TOP100.tsv")
    write_tsv(combined_kegg_top100, combined_kegg_top100_filename)
    
    # Save significant KEGG pathways only
    combined_kegg_sig <- combined_kegg %>% 
      dplyr::filter(p.adjust < 0.05)
    if (nrow(combined_kegg_sig) > 0) {
      combined_kegg_sig_filename <- file.path(combined_dir, "ALL_ANALYSES_KEGG_enrichment_SIGNIFICANT.tsv")
      write_tsv(combined_kegg_sig, combined_kegg_sig_filename)
    }
    
    cat("Combined KEGG results saved:\n")
    cat("  - All results:", combined_kegg_filename, "\n")
    cat("  - Top 100:", combined_kegg_top100_filename, "\n")
    if (nrow(combined_kegg_sig) > 0) {
      cat("  - Significant only:", combined_kegg_sig_filename, "\n")
    }
  }
  
  # Create comprehensive summary statistics
  summary_stats <- list()
  
  if (length(all_go_results) > 0) {
    combined_go <- dplyr::bind_rows(all_go_results)
    summary_stats$go <- list(
      total_terms = nrow(combined_go),
      significant_terms = sum(combined_go$p.adjust < 0.05, na.rm = TRUE),
      analyses_count = length(all_go_results),
      contrasts_count = length(unique(combined_go$contrast)),
      top_terms = combined_go %>% dplyr::slice_max(order_by = log_padj, n = 20)
    )
  }
  
  if (length(all_kegg_results) > 0) {
    combined_kegg <- dplyr::bind_rows(all_kegg_results)
    summary_stats$kegg <- list(
      total_pathways = nrow(combined_kegg),
      significant_pathways = sum(combined_kegg$p.adjust < 0.05, na.rm = TRUE),
      analyses_count = length(all_kegg_results),
      contrasts_count = length(unique(combined_kegg$contrast)),
      top_pathways = combined_kegg %>% dplyr::slice_max(order_by = log_padj, n = 20)
    )
  }
  
  # Save summary statistics
  summary_stats_filename <- file.path(combined_dir, "ALL_ANALYSES_enrichment_summary_stats.rds")
  saveRDS(summary_stats, summary_stats_filename)
  
  # Create text summary
  summary_text <- paste0(
    "=== COMBINED ENRICHMENT ANALYSIS SUMMARY ===\n",
    "Date: ", format(Sys.time(), "%Y-%m-%d %H:%M:%S"), "\n",
    "Analyses included: ", paste(names(enrichment_results), collapse = ", "), "\n\n",
    
    "GO ENRICHMENT SUMMARY:\n",
    ifelse(length(all_go_results) > 0,
           paste0("  Total terms analyzed: ", summary_stats$go$total_terms, "\n",
                  "  Significant terms (padj < 0.05): ", summary_stats$go$significant_terms, "\n",
                  "  Analyses included: ", summary_stats$go$analyses_count, "\n",
                  "  Contrasts analyzed: ", summary_stats$go$contrasts_count, "\n"),
           "  No GO results available\n"),
    "\n",
    
    "KEGG ENRICHMENT SUMMARY:\n",
    ifelse(length(all_kegg_results) > 0,
           paste0("  Total pathways analyzed: ", summary_stats$kegg$total_pathways, "\n",
                  "  Significant pathways (padj < 0.05): ", summary_stats$kegg$significant_pathways, "\n",
                  "  Analyses included: ", summary_stats$kegg$analyses_count, "\n",
                  "  Contrasts analyzed: ", summary_stats$kegg$contrasts_count, "\n"),
           "  No KEGG results available\n"),
    "\n",
    
    "FILES CREATED:\n",
    "  - ALL_ANALYSES_GO_enrichment_ALL.tsv (all GO results)\n",
    "  - ALL_ANALYSES_GO_enrichment_TOP100.tsv (top 100 GO terms)\n",
    "  - ALL_ANALYSES_GO_enrichment_SIGNIFICANT.tsv (significant GO terms only)\n",
    "  - ALL_ANALYSES_KEGG_enrichment_ALL.tsv (all KEGG results)\n",
    "  - ALL_ANALYSES_KEGG_enrichment_TOP100.tsv (top 100 KEGG pathways)\n",
    "  - ALL_ANALYSES_KEGG_enrichment_SIGNIFICANT.tsv (significant KEGG pathways only)\n",
    "  - ALL_ANALYSES_enrichment_summary_stats.rds (summary statistics)\n",
    "  - This text summary\n"
  )
  
  summary_filename <- file.path(combined_dir, "ALL_ANALYSES_enrichment_summary.txt")
  writeLines(summary_text, summary_filename)
  
  cat("\nCombined enrichment summary saved to:", combined_dir, "\n")
  cat("Summary statistics saved to:", summary_stats_filename, "\n")
  cat("Text summary saved to:", summary_filename, "\n")
}

Import Data

# Read in metadata sheet
Metadata <- readxl::read_excel(here::here("Data", "Transcriptomics", "Data", "ROL_MajorExperiment__MetadataSheet__Corrected_05092025.xlsx"))

# Read in SummarizedExperiment object
se <- readRDS(here::here("Data", "Transcriptomics", "Results", "rnaseq", "051525", "salmon", "salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds"))

# Print basic information about the dataset
cat("Number of genes:", nrow(se), "\n")

## Number of genes: 39447

cat("Number of samples:", ncol(se), "\n")

## Number of samples: 72

cat("Sample names:", colnames(se), "\n")

## Sample names: TS047_RoL_RNA_110 TS047_RoL_RNA_112 TS047_RoL_RNA_114 TS047_RoL_RNA_116 TS047_RoL_RNA_119 TS047_RoL_RNA_136 TS047_RoL_RNA_142 TS047_RoL_RNA_145 TS047_RoL_RNA_146 TS047_RoL_RNA_16 TS047_RoL_RNA_170 TS047_RoL_RNA_175 TS047_RoL_RNA_177 TS047_RoL_RNA_20 TS047_RoL_RNA_200 TS047_RoL_RNA_204 TS047_RoL_RNA_229 TS047_RoL_RNA_231 TS047_RoL_RNA_258 TS047_RoL_RNA_262 TS047_RoL_RNA_286 TS047_RoL_RNA_288 TS047_RoL_RNA_289 TS047_RoL_RNA_291 TS047_RoL_RNA_317 TS047_RoL_RNA_318 TS047_RoL_RNA_319 TS047_RoL_RNA_322 TS047_RoL_RNA_326 TS047_RoL_RNA_328 TS047_RoL_RNA_347 TS047_RoL_RNA_355 TS047_RoL_RNA_377 TS047_RoL_RNA_381 TS047_RoL_RNA_407 TS047_RoL_RNA_412 TS047_RoL_RNA_439 TS047_RoL_RNA_442 TS047_RoL_RNA_46 TS047_RoL_RNA_468 TS047_RoL_RNA_469 TS047_RoL_RNA_477 TS047_RoL_RNA_478 TS047_RoL_RNA_498 TS047_RoL_RNA_500 TS047_RoL_RNA_502 TS047_RoL_RNA_506 TS047_RoL_RNA_51 TS047_RoL_RNA_526 TS047_RoL_RNA_528 TS047_RoL_RNA_530 TS047_RoL_RNA_532 TS047_RoL_RNA_559 TS047_RoL_RNA_561 TS047_RoL_RNA_562 TS047_RoL_RNA_586 TS047_RoL_RNA_616 TS047_RoL_RNA_618 TS047_RoL_RNA_646 TS047_RoL_RNA_651 TS047_RoL_RNA_652 TS047_RoL_RNA_655 TS047_RoL_RNA_676 TS047_RoL_RNA_677 TS047_RoL_RNA_678 TS047_RoL_RNA_679 TS047_RoL_RNA_683 TS047_RoL_RNA_707 TS047_RoL_RNA_708 TS047_RoL_RNA_710 TS047_RoL_RNA_79 TS047_RoL_RNA_85

cat("Available assays:", assayNames(se), "\n")

## Available assays: counts abundance

cat("Column data (metadata):", names(colData(se)), "\n")

## Column data (metadata): sample fastq_1 fastq_2 strandedness

Data Preprocessing

# Clean sample names by removing "TS047_RoL_RNA_" prefix
clean_names <- gsub("TS047_RoL_RNA_", "", colnames(se))

# Update column names in the SummarizedExperiment object
colnames(se) <- clean_names

# Correct specific sample names if needed
# Rename sample 136 to 138
clean_names[clean_names == "136"] <- "138"
colnames(se) <- clean_names

# Create a data frame for the metadata columns we want to add
metadata_cols <- c("Time", "Antibiotics", "Temperature", 
                  "Pathogen", "History", "Length.mm", "Weight.g", "Total.Worm.Count")

# Initialize a data frame to store the metadata
sample_metadata <- data.frame(
  Sample_Name = clean_names,
  stringsAsFactors = FALSE
)
rownames(sample_metadata) <- clean_names

# Add each metadata column
for (col in metadata_cols) {
  values <- rep(NA, length(clean_names))
  
  for (i in seq_along(clean_names)) {
    matches <- which(Metadata$Sample_Name == clean_names[i])
    
    if (length(matches) == 1) {
      values[i] <- Metadata[matches, col, drop = TRUE]
    }
  }
  
  sample_metadata[[col]] <- values
}

# Add the metadata to the SummarizedExperiment object
colData(se) <- DataFrame(sample_metadata)

cat("Metadata added to SummarizedExperiment object\n")

## Metadata added to SummarizedExperiment object

Create DESeq2 Dataset

# Remove samples with NA values in treatment columns
se_filtered <- se[, !is.na(colData(se)$Antibiotics) & !is.na(colData(se)$Temperature) & !is.na(colData(se)$Pathogen)]
cat("Number of samples after removing NAs:", ncol(se_filtered), "\n")

## Number of samples after removing NAs: 71

# Create treatment combinations using DESeq2-compatible format
colData(se_filtered)$Treatment <- paste0(
  ifelse(colData(se_filtered)$Antibiotics == 1, "A_plus", "A_minus"), "_",
  ifelse(colData(se_filtered)$Temperature == 1, "T_plus", "T_minus"), "_",
  ifelse(colData(se_filtered)$Pathogen == 1, "P_plus", "P_minus")
)

# Create plotting-friendly treatment names
colData(se_filtered)$Treatment_Plot <- paste0(
  ifelse(colData(se_filtered)$Antibiotics == 1, "A+", "A-"), " ",
  ifelse(colData(se_filtered)$Temperature == 1, "T+", "T-"), " ",
  ifelse(colData(se_filtered)$Pathogen == 1, "P+", "P-")
)

# Convert treatment to factor with specified order (DESeq2 names)
colData(se_filtered)$Treatment <- factor(colData(se_filtered)$Treatment, levels = treatment_order_deseq)

# Convert plotting treatment to factor with specified order
colData(se_filtered)$Treatment_Plot <- factor(colData(se_filtered)$Treatment_Plot, levels = treatment_order_plot)

# Print the distribution of treatment combinations
cat("\nTreatment combination distribution:\n")

## 
## Treatment combination distribution:

print(table(colData(se_filtered)$Treatment))

## 
## A_minus_T_minus_P_minus  A_minus_T_minus_P_plus  A_plus_T_minus_P_minus 
##                       6                      11                       6 
##   A_plus_T_minus_P_plus  A_minus_T_plus_P_minus   A_minus_T_plus_P_plus 
##                      12                       6                      12 
##   A_plus_T_plus_P_minus    A_plus_T_plus_P_plus 
##                       6                      12

print(table(colData(se_filtered)$Treatment_Plot))

## 
## A- T- P- A- T- P+ A+ T- P- A+ T- P+ A- T+ P- A- T+ P+ A+ T+ P- A+ T+ P+ 
##        6       11        6       12        6       12        6       12

# Clean other factor levels
colData(se_filtered)$Time <- factor(colData(se_filtered)$Time)
colData(se_filtered)$Antibiotics <- factor(colData(se_filtered)$Antibiotics)
colData(se_filtered)$Temperature <- factor(colData(se_filtered)$Temperature)
colData(se_filtered)$Pathogen <- factor(colData(se_filtered)$Pathogen)

# Create initial design formula
design_formula <- ~ Treatment

# Use length-scaled counts for DESeq2 analysis
if (!"counts" %in% assayNames(se_filtered)) {
  # Read in the length-scaled counts file
  length_scaled_counts <- read.table(here::here("Data", "Transcriptomics", "Results", "rnaseq", "051525", "salmon", "salmon.merged.gene_counts_length_scaled.tsv"), 
                          header = TRUE, row.names = 1) 
  
  # Convert to matrix and ensure it's numeric
  counts_matrix <- as.matrix(length_scaled_counts)
  mode(counts_matrix) <- "numeric"
  
  # Round to nearest integer (DESeq2 requires integer counts)
  counts_matrix <- round(counts_matrix)
  
  # Ensure the order of samples matches the SummarizedExperiment
  counts_matrix <- counts_matrix[, colnames(se_filtered)]
} else {
  # If counts are available, use them
  counts_matrix <- as.matrix(assays(se_filtered)$counts)
  mode(counts_matrix) <- "numeric"
  counts_matrix <- round(counts_matrix)
}

# Create initial DESeq2 dataset
dds_initial <- DESeqDataSetFromMatrix(
  countData = counts_matrix,
  colData = colData(se_filtered),
  design = design_formula
)

## converting counts to integer mode

# Pre-filtering: remove low abundance transcripts
cpm <- counts(dds_initial) / colSums(counts(dds_initial)) * 1e6

# Keep genes that have at least 2 CPM in at least 3 samples
keep <- rowSums(cpm >= 2) >= 3

dds_filtered <- dds_initial[keep,]

# Print filtering statistics
cat("Number of genes before filtering:", nrow(counts_matrix), "\n")

## Number of genes before filtering: 39447

cat("Number of genes after filtering:", nrow(dds_filtered), "\n")

## Number of genes after filtering: 20664

cat("Number of genes removed:", nrow(counts_matrix) - nrow(dds_filtered), "\n")

## Number of genes removed: 18783

cat("Percentage of genes kept:", round(nrow(dds_filtered)/nrow(counts_matrix)*100, 2), "%\n")

## Percentage of genes kept: 52.38 %

# Transform counts for visualization
rld <- vst(dds_filtered, blind=FALSE)

# Estimate size factors
dds_filtered <- estimateSizeFactors(dds_filtered)

# Get normalized counts
normalized_counts <- counts(dds_filtered, normalized=TRUE)

# After dds_filtered is created and before any downstream analyses:

# List of genes to exclude
genes_to_exclude <- c(
  "zgc:112970",
  "lectin",
  "zp2.6",
  "qdprb.4",
  "bncr",
  "avd",
  "tdgf1",
  "adad2",
  "LOC137488852",
  "ppt2a.1",
  "snapc1a",
  "exd1",
  "LOC141381090",
  "LOC141381093",
  "LOC141378343",
  "LOC101884348"
)

# Remove these genes from dds_filtered, rld, and normalized_counts
keep_genes <- !(rownames(dds_filtered) %in% genes_to_exclude)
dds_filtered <- dds_filtered[keep_genes, ]

# Re-transform counts for visualization after filtering
rld <- vst(dds_filtered, blind=FALSE)

# Estimate size factors again after filtering
dds_filtered <- estimateSizeFactors(dds_filtered)

# Get normalized counts after filtering
normalized_counts <- counts(dds_filtered, normalized=TRUE)

# Print exclusion summary
cat("Number of genes excluded:", length(genes_to_exclude), "\n")

## Number of genes excluded: 16

cat("Number of genes remaining after exclusion:", nrow(dds_filtered), "\n")

## Number of genes remaining after exclusion: 20648

Set up parallel processing

# Enhanced parallel processing setup
# Detect number of available cores
available_cores <- parallel::detectCores()
cat("Available cores:", available_cores, "\n")

## Available cores: 10

# Use 75% of available cores to avoid overwhelming the system
# Leave some cores free for other processes
num_cores <- max(1, floor(available_cores * 0.75))
cat("Using cores for parallel processing:", num_cores, "\n")

## Using cores for parallel processing: 7

# Create optimized BiocParallel parameters
bp_param <- MulticoreParam(
  workers = num_cores,
  tasks = num_cores * 2,  # Increase task granularity
  progressbar = TRUE      # Enable progress reporting
)

# Register the optimized parameters
register(bp_param)

cat("Parallel processing configured with", num_cores, "cores\n")

## Parallel processing configured with 7 cores

cat("Task granularity:", bp_param$tasks, "\n")

## Task granularity: 14

cat("Progress bar enabled:", bp_param$progressbar, "\n")

## Progress bar enabled: TRUE

Define Analysis Comparisons

# Define the specific comparisons for our analysis
comparisons <- list(
  
  # 1. All Treatment Groups (comprehensive analysis)
  "All_Treatments" = list(
    description = "Comprehensive analysis across all treatment combinations",
    design = ~ Treatment,
    contrasts = list(
      "A_minus_T_minus_P_plus_vs_A_minus_T_minus_P_minus" = c("Treatment", "A_minus_T_minus_P_plus", "A_minus_T_minus_P_minus"),
      "A_plus_T_minus_P_minus_vs_A_minus_T_minus_P_minus" = c("Treatment", "A_plus_T_minus_P_minus", "A_minus_T_minus_P_minus"),
      "A_plus_T_minus_P_plus_vs_A_minus_T_minus_P_minus" = c("Treatment", "A_plus_T_minus_P_plus", "A_minus_T_minus_P_minus"),
      "A_minus_T_plus_P_minus_vs_A_minus_T_minus_P_minus" = c("Treatment", "A_minus_T_plus_P_minus", "A_minus_T_minus_P_minus"),
      "A_minus_T_plus_P_plus_vs_A_minus_T_minus_P_minus" = c("Treatment", "A_minus_T_plus_P_plus", "A_minus_T_minus_P_minus"),
      "A_plus_T_plus_P_minus_vs_A_minus_T_minus_P_minus" = c("Treatment", "A_plus_T_plus_P_minus", "A_minus_T_minus_P_minus"),
      "A_plus_T_plus_P_plus_vs_A_minus_T_minus_P_minus" = c("Treatment", "A_plus_T_plus_P_plus", "A_minus_T_minus_P_minus")
    )
  ),
  
  # 2. Parasite Effect (A_minus_T_minus_P_minus vs A_minus_T_minus_P_plus)
  "Parasite_Effect" = list(
    description = "Baseline parasite effect: A_minus_T_minus_P_minus vs A_minus_T_minus_P_plus",
    design = ~ Treatment,
    contrasts = list(
      "A_minus_T_minus_P_plus_vs_A_minus_T_minus_P_minus" = c("Treatment", "A_minus_T_minus_P_plus", "A_minus_T_minus_P_minus")
    )
  ),
  
  # 3. Historical Contingency (A_minus_T_minus_P_plus vs A_plus_T_minus_P_plus, A_minus_T_plus_P_plus, A_plus_T_plus_P_plus)
  "Historical_Contingency" = list(
    description = "How prior stressors affect parasite response: A_minus_T_minus_P_plus vs (A_plus_T_minus_P_plus, A_minus_T_plus_P_plus, A_plus_T_plus_P_plus)",
    design = ~ Treatment,
    contrasts = list(
      "A_plus_T_minus_P_plus_vs_A_minus_T_minus_P_plus" = c("Treatment", "A_plus_T_minus_P_plus", "A_minus_T_minus_P_plus"),
      "A_minus_T_plus_P_plus_vs_A_minus_T_minus_P_plus" = c("Treatment", "A_minus_T_plus_P_plus", "A_minus_T_minus_P_plus"),
      "A_plus_T_plus_P_plus_vs_A_minus_T_minus_P_plus" = c("Treatment", "A_plus_T_plus_P_plus", "A_minus_T_minus_P_plus")
    )
  ),
  
  # 4. Recovery Analysis (A_minus_T_minus_P_minus vs A_plus_T_minus_P_minus, A_minus_T_plus_P_minus, A_plus_T_plus_P_minus)
  "Recovery_Analysis" = list(
    description = "How prior stressors affect recovery: A_minus_T_minus_P_minus vs (A_plus_T_minus_P_minus, A_minus_T_plus_P_minus, A_plus_T_plus_P_minus)",
    design = ~ Treatment,
    contrasts = list(
      "A_plus_T_minus_P_minus_vs_A_minus_T_minus_P_minus" = c("Treatment", "A_plus_T_minus_P_minus", "A_minus_T_minus_P_minus"),
      "A_minus_T_plus_P_minus_vs_A_minus_T_minus_P_minus" = c("Treatment", "A_minus_T_plus_P_minus", "A_minus_T_minus_P_minus"),
      "A_plus_T_plus_P_minus_vs_A_minus_T_minus_P_minus" = c("Treatment", "A_plus_T_plus_P_minus", "A_minus_T_minus_P_minus")
    )
  )
)

Code

(hide)

Quality Control

Sample Distance Heatmap

Principal Component Analysis

## using ntop=500 top features by variance

Manage Saved Results

# Check which analyses have saved results
cat("=== Checking for saved results ===\n")

## === Checking for saved results ===

for (analysis_name in names(comparisons)) {
  if (results_exist(analysis_name)) {
    cat("✓", analysis_name, "- results found\n")
  } else {
    cat("✗", analysis_name, "- no saved results\n")
  }
}

## ✓ All_Treatments - results found
## ✓ Parasite_Effect - results found
## ✓ Historical_Contingency - results found
## ✓ Recovery_Analysis - results found

# Set this to TRUE if you want to recompute all analyses
# Set to FALSE to use existing results when available
force_recompute_all <- FALSE

# You can also set individual analyses to recompute
force_recompute_individual <- list(
  "All_Treatments" = FALSE,
  "Parasite_Effect" = FALSE,
  "Historical_Contingency" = FALSE,
  "Recovery_Analysis" = FALSE
)

cat("\nForce recompute all:", force_recompute_all, "\n")

## 
## Force recompute all: FALSE

cat("Individual force recompute settings:\n")

## Individual force recompute settings:

for (analysis_name in names(force_recompute_individual)) {
  cat("  ", analysis_name, ":", force_recompute_individual[[analysis_name]], "\n")
}

##    All_Treatments : FALSE 
##    Parasite_Effect : FALSE 
##    Historical_Contingency : FALSE 
##    Recovery_Analysis : FALSE

# Uncomment the lines below if you want to clean up saved results
# cleanup_saved_results()  # Remove all saved results
# cleanup_saved_results(c("All_Treatments", "Parasite_Effect"))  # Remove specific analyses

cat("\n=== Usage Instructions ===\n")

## 
## === Usage Instructions ===

cat("1. Set force_recompute_all = TRUE to recompute all analyses\n")

## 1. Set force_recompute_all = TRUE to recompute all analyses

cat("2. Set individual force_recompute_individual values to TRUE to recompute specific analyses\n")

## 2. Set individual force_recompute_individual values to TRUE to recompute specific analyses

cat("3. Use cleanup_saved_results() to remove all saved results\n")

## 3. Use cleanup_saved_results() to remove all saved results

cat("4. Use cleanup_saved_results(c('analysis1', 'analysis2')) to remove specific analyses\n")

## 4. Use cleanup_saved_results(c('analysis1', 'analysis2')) to remove specific analyses

Run DESeq2 Analyses

# Monitor initial performance
cat("=== Starting DESeq2 Analysis ===\n")

## === Starting DESeq2 Analysis ===

monitor_performance()

## === Performance Monitor ===
## Memory usage:
##            used  (Mb) gc trigger  (Mb) limit (Mb) max used  (Mb)
## Ncells  8802039 470.1   16282930 869.7         NA 16282930 869.7
## Vcells 32613476 248.9   57073799 435.5      32768 47494646 362.4
## CPU info:
## CPU usage: 18.44% user, 22.63% sys, 58.91% idle  
## Active parallel workers: 7 
## ========================

# Optimize memory before starting
optimize_memory()

## Optimizing memory usage...
## Memory optimization complete

# Run all analyses
all_results <- list()

for (analysis_name in names(comparisons)) {
  cat("\n--- Starting analysis:", analysis_name, "---\n")
  
  # Monitor performance before each analysis
  monitor_performance()
  
  # Run the analysis
  all_results[[analysis_name]] <- run_analysis_set(analysis_name, comparisons[[analysis_name]], force_recompute_all || force_recompute_individual[[analysis_name]])
  
  # Optimize memory after each analysis
  optimize_memory()
  
  cat("--- Completed analysis:", analysis_name, "---\n")
}

## 
## --- Starting analysis: All_Treatments ---
## === Performance Monitor ===
## Memory usage:
##            used  (Mb) gc trigger  (Mb) limit (Mb) max used  (Mb)
## Ncells  8802192 470.1   16282930 869.7         NA 16282930 869.7
## Vcells 32614304 248.9   57073799 435.5      32768 47494646 362.4
## CPU info:
## CPU usage: 11.85% user, 11.73% sys, 76.41% idle  
## Active parallel workers: 7 
## ========================
## 
## === Running All_Treatments ===
## Description: Comprehensive analysis across all treatment combinations 
## Loading existing results for All_Treatments 
## Loading existing results for: All_Treatments 
## Optimizing memory usage...
## Memory optimization complete
## --- Completed analysis: All_Treatments ---
## 
## --- Starting analysis: Parasite_Effect ---
## === Performance Monitor ===
## Memory usage:
##            used  (Mb) gc trigger  (Mb) limit (Mb) max used  (Mb)
## Ncells  8803051 470.2   16282930 869.7         NA 16282930 869.7
## Vcells 33630989 256.6   57073799 435.5      32768 47494646 362.4
## CPU info:
## CPU usage: 18.91% user, 13.93% sys, 67.14% idle  
## Active parallel workers: 7 
## ========================
## 
## === Running Parasite_Effect ===
## Description: Baseline parasite effect: A_minus_T_minus_P_minus vs A_minus_T_minus_P_plus 
## Loading existing results for Parasite_Effect 
## Loading existing results for: Parasite_Effect 
## Optimizing memory usage...
## Memory optimization complete
## --- Completed analysis: Parasite_Effect ---
## 
## --- Starting analysis: Historical_Contingency ---
## === Performance Monitor ===
## Memory usage:
##            used  (Mb) gc trigger  (Mb) limit (Mb) max used  (Mb)
## Ncells  8803190 470.2   16282930 869.7         NA 16282930 869.7
## Vcells 33776293 257.7   57073799 435.5      32768 47494646 362.4
## CPU info:
## CPU usage: 10.76% user, 11.12% sys, 78.10% idle  
## Active parallel workers: 7 
## ========================
## 
## === Running Historical_Contingency ===
## Description: How prior stressors affect parasite response: A_minus_T_minus_P_plus vs (A_plus_T_minus_P_plus, A_minus_T_plus_P_plus, A_plus_T_plus_P_plus) 
## Loading existing results for Historical_Contingency 
## Loading existing results for: Historical_Contingency 
## Optimizing memory usage...
## Memory optimization complete
## --- Completed analysis: Historical_Contingency ---
## 
## --- Starting analysis: Recovery_Analysis ---
## === Performance Monitor ===
## Memory usage:
##            used  (Mb) gc trigger  (Mb) limit (Mb) max used  (Mb)
## Ncells  8803415 470.2   16282930 869.7         NA 16282930 869.7
## Vcells 34211196 261.1   57073799 435.5      32768 47494646 362.4
## CPU info:
## CPU usage: 12.82% user, 13.69% sys, 73.48% idle  
## Active parallel workers: 7 
## ========================
## 
## === Running Recovery_Analysis ===
## Description: How prior stressors affect recovery: A_minus_T_minus_P_minus vs (A_plus_T_minus_P_minus, A_minus_T_plus_P_minus, A_plus_T_plus_P_minus) 
## Loading existing results for Recovery_Analysis 
## Loading existing results for: Recovery_Analysis 
## Optimizing memory usage...
## Memory optimization complete
## --- Completed analysis: Recovery_Analysis ---

# Final performance check
cat("\n=== Final Performance Check ===\n")

## 
## === Final Performance Check ===

monitor_performance()

## === Performance Monitor ===
## Memory usage:
##            used  (Mb) gc trigger  (Mb) limit (Mb) max used  (Mb)
## Ncells  8803577 470.2   16282930 869.7         NA 16282930 869.7
## Vcells 34645555 264.4   57073799 435.5      32768 47494646 362.4
## CPU info:
## CPU usage: 12.24% user, 12.36% sys, 75.39% idle  
## Active parallel workers: 7 
## ========================

# Print summary of results
cat("\n=== Analysis Summary ===\n")

## 
## === Analysis Summary ===

for (analysis_name in names(all_results)) {
  cat("\n", analysis_name, ":\n")
  for (contrast_name in names(all_results[[analysis_name]])) {
    res <- all_results[[analysis_name]][[contrast_name]]
    cat("  ", contrast_name, ":\n")
    cat("    Significant genes (padj < 0.05):", sum(res$padj < 0.05, na.rm=TRUE), "\n")
    cat("    Upregulated genes:", sum(res$padj < 0.05 & res$log2FoldChange > 0, na.rm=TRUE), "\n")
    cat("    Downregulated genes:", sum(res$padj < 0.05 & res$log2FoldChange < 0, na.rm=TRUE), "\n")
  }
}

## 
##  All_Treatments :
##    A_minus_T_minus_P_plus_vs_A_minus_T_minus_P_minus :
##     Significant genes (padj < 0.05): 3753 
##     Upregulated genes: 1994 
##     Downregulated genes: 1759 
##    A_plus_T_minus_P_minus_vs_A_minus_T_minus_P_minus :
##     Significant genes (padj < 0.05): 35 
##     Upregulated genes: 8 
##     Downregulated genes: 27 
##    A_plus_T_minus_P_plus_vs_A_minus_T_minus_P_minus :
##     Significant genes (padj < 0.05): 6473 
##     Upregulated genes: 3453 
##     Downregulated genes: 3020 
##    A_minus_T_plus_P_minus_vs_A_minus_T_minus_P_minus :
##     Significant genes (padj < 0.05): 47 
##     Upregulated genes: 6 
##     Downregulated genes: 41 
##    A_minus_T_plus_P_plus_vs_A_minus_T_minus_P_minus :
##     Significant genes (padj < 0.05): 6196 
##     Upregulated genes: 3235 
##     Downregulated genes: 2961 
##    A_plus_T_plus_P_minus_vs_A_minus_T_minus_P_minus :
##     Significant genes (padj < 0.05): 117 
##     Upregulated genes: 18 
##     Downregulated genes: 99 
##    A_plus_T_plus_P_plus_vs_A_minus_T_minus_P_minus :
##     Significant genes (padj < 0.05): 5017 
##     Upregulated genes: 2603 
##     Downregulated genes: 2414 
## 
##  Parasite_Effect :
##    A_minus_T_minus_P_plus_vs_A_minus_T_minus_P_minus :
##     Significant genes (padj < 0.05): 3753 
##     Upregulated genes: 1994 
##     Downregulated genes: 1759 
## 
##  Historical_Contingency :
##    A_plus_T_minus_P_plus_vs_A_minus_T_minus_P_plus :
##     Significant genes (padj < 0.05): 49 
##     Upregulated genes: 26 
##     Downregulated genes: 23 
##    A_minus_T_plus_P_plus_vs_A_minus_T_minus_P_plus :
##     Significant genes (padj < 0.05): 137 
##     Upregulated genes: 93 
##     Downregulated genes: 44 
##    A_plus_T_plus_P_plus_vs_A_minus_T_minus_P_plus :
##     Significant genes (padj < 0.05): 18 
##     Upregulated genes: 5 
##     Downregulated genes: 13 
## 
##  Recovery_Analysis :
##    A_plus_T_minus_P_minus_vs_A_minus_T_minus_P_minus :
##     Significant genes (padj < 0.05): 35 
##     Upregulated genes: 8 
##     Downregulated genes: 27 
##    A_minus_T_plus_P_minus_vs_A_minus_T_minus_P_minus :
##     Significant genes (padj < 0.05): 47 
##     Upregulated genes: 6 
##     Downregulated genes: 41 
##    A_plus_T_plus_P_minus_vs_A_minus_T_minus_P_minus :
##     Significant genes (padj < 0.05): 117 
##     Upregulated genes: 18 
##     Downregulated genes: 99

Results Overview

Heatmap

## Number of genes excluded: 16 
## Number of genes remaining in top_genes_list: 95

Sig Genes

00) All Treatment Groups Analysis

Sig Genes

Volcano Plots

Summary Tables

summary_table

Summary of Differential Gene Expression
All Treatment Groups Analysis
Treatment Comparison	Total Genes	Significant Genes	Upregulated	Downregulated
A_minus_T_minus_P_plus_vs_A_minus_T_minus_P_minus	20,648	3,753	1,994	1,759
A_plus_T_minus_P_minus_vs_A_minus_T_minus_P_minus	20,648	35	8	27
A_plus_T_minus_P_plus_vs_A_minus_T_minus_P_minus	20,648	6,473	3,453	3,020
A_minus_T_plus_P_minus_vs_A_minus_T_minus_P_minus	20,648	47	6	41
A_minus_T_plus_P_plus_vs_A_minus_T_minus_P_minus	20,648	6,196	3,235	2,961
A_plus_T_plus_P_minus_vs_A_minus_T_minus_P_minus	20,648	117	18	99
A_plus_T_plus_P_plus_vs_A_minus_T_minus_P_minus	20,648	5,017	2,603	2,414

Top Genes Tables

## ### Top 10 Upregulated Genes: A_minus_T_minus_P_plus_vs_A_minus_T_minus_P_minus 
## ### Top 10 Downregulated Genes: A_minus_T_minus_P_plus_vs_A_minus_T_minus_P_minus 
## ### Top 10 Upregulated Genes: A_plus_T_minus_P_minus_vs_A_minus_T_minus_P_minus 
## ### Top 10 Downregulated Genes: A_plus_T_minus_P_minus_vs_A_minus_T_minus_P_minus 
## ### Top 10 Upregulated Genes: A_plus_T_minus_P_plus_vs_A_minus_T_minus_P_minus 
## ### Top 10 Downregulated Genes: A_plus_T_minus_P_plus_vs_A_minus_T_minus_P_minus 
## ### Top 10 Upregulated Genes: A_minus_T_plus_P_minus_vs_A_minus_T_minus_P_minus 
## ### Top 10 Downregulated Genes: A_minus_T_plus_P_minus_vs_A_minus_T_minus_P_minus 
## ### Top 10 Upregulated Genes: A_minus_T_plus_P_plus_vs_A_minus_T_minus_P_minus 
## ### Top 10 Downregulated Genes: A_minus_T_plus_P_plus_vs_A_minus_T_minus_P_minus 
## ### Top 10 Upregulated Genes: A_plus_T_plus_P_minus_vs_A_minus_T_minus_P_minus 
## ### Top 10 Downregulated Genes: A_plus_T_plus_P_minus_vs_A_minus_T_minus_P_minus 
## ### Top 10 Upregulated Genes: A_plus_T_plus_P_plus_vs_A_minus_T_minus_P_minus 
## ### Top 10 Downregulated Genes: A_plus_T_plus_P_plus_vs_A_minus_T_minus_P_minus

01) Parasite Effect Analysis

Sig Genes

Volcano Plot

Summary Table

summary_table

Summary of Differential Gene Expression
Parasite Effect Analysis (A- T- P- vs A- T- P+)
Treatment Comparison	Total Genes	Significant Genes	Upregulated	Downregulated
A_minus_T_minus_P_plus_vs_A_minus_T_minus_P_minus	20,648	3,753	1,994	1,759

Top Genes Table

## ### Top 20 Significant Genes: A_minus_T_minus_P_plus_vs_A_minus_T_minus_P_minus 
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##   <thead>
##     <tr class="gt_heading">
##       <td colspan="4" class="gt_heading gt_title gt_font_normal gt_bottom_border" style>Top 20 Significant Genes: Parasite Effect</td>
##     </tr>
##     
##     <tr class="gt_col_headings">
##       <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="Gene">Gene</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="log2 Fold Change">log2 Fold Change</th>
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##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="Base Mean">Base Mean</th>
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##     <tr><td headers="gene" class="gt_row gt_left">gbp1</td>
## <td headers="log2FoldChange" class="gt_row gt_right">3.78</td>
## <td headers="padj" class="gt_row gt_right">2.550 × 10<sup style='font-size: 65%;'>−15</sup></td>
## <td headers="baseMean" class="gt_row gt_right">4,447.72</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">zgc:110540</td>
## <td headers="log2FoldChange" class="gt_row gt_right">2.92</td>
## <td headers="padj" class="gt_row gt_right">1.337 × 10<sup style='font-size: 65%;'>−13</sup></td>
## <td headers="baseMean" class="gt_row gt_right">174.69</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">ercc6l</td>
## <td headers="log2FoldChange" class="gt_row gt_right">2.70</td>
## <td headers="padj" class="gt_row gt_right">2.107 × 10<sup style='font-size: 65%;'>−13</sup></td>
## <td headers="baseMean" class="gt_row gt_right">250.82</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">tapbpl</td>
## <td headers="log2FoldChange" class="gt_row gt_right">1.97</td>
## <td headers="padj" class="gt_row gt_right">2.296 × 10<sup style='font-size: 65%;'>−13</sup></td>
## <td headers="baseMean" class="gt_row gt_right">718.48</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">batf2</td>
## <td headers="log2FoldChange" class="gt_row gt_right">4.57</td>
## <td headers="padj" class="gt_row gt_right">1.618 × 10<sup style='font-size: 65%;'>−12</sup></td>
## <td headers="baseMean" class="gt_row gt_right">462.49</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">LOC101885672</td>
## <td headers="log2FoldChange" class="gt_row gt_right">4.69</td>
## <td headers="padj" class="gt_row gt_right">2.264 × 10<sup style='font-size: 65%;'>−12</sup></td>
## <td headers="baseMean" class="gt_row gt_right">1,001.46</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">gbp2</td>
## <td headers="log2FoldChange" class="gt_row gt_right">2.74</td>
## <td headers="padj" class="gt_row gt_right">3.086 × 10<sup style='font-size: 65%;'>−12</sup></td>
## <td headers="baseMean" class="gt_row gt_right">978.30</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">pcna</td>
## <td headers="log2FoldChange" class="gt_row gt_right">1.83</td>
## <td headers="padj" class="gt_row gt_right">3.971 × 10<sup style='font-size: 65%;'>−12</sup></td>
## <td headers="baseMean" class="gt_row gt_right">2,492.46</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">zgc:101715</td>
## <td headers="log2FoldChange" class="gt_row gt_right">2.32</td>
## <td headers="padj" class="gt_row gt_right">6.316 × 10<sup style='font-size: 65%;'>−12</sup></td>
## <td headers="baseMean" class="gt_row gt_right">456.29</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">anxa3b</td>
## <td headers="log2FoldChange" class="gt_row gt_right">2.20</td>
## <td headers="padj" class="gt_row gt_right">3.440 × 10<sup style='font-size: 65%;'>−11</sup></td>
## <td headers="baseMean" class="gt_row gt_right">3,058.49</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">irf10</td>
## <td headers="log2FoldChange" class="gt_row gt_right">2.64</td>
## <td headers="padj" class="gt_row gt_right">5.490 × 10<sup style='font-size: 65%;'>−11</sup></td>
## <td headers="baseMean" class="gt_row gt_right">568.74</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">dut</td>
## <td headers="log2FoldChange" class="gt_row gt_right">2.13</td>
## <td headers="padj" class="gt_row gt_right">5.818 × 10<sup style='font-size: 65%;'>−11</sup></td>
## <td headers="baseMean" class="gt_row gt_right">513.03</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">rab40b</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−2.10</td>
## <td headers="padj" class="gt_row gt_right">1.622 × 10<sup style='font-size: 65%;'>−10</sup></td>
## <td headers="baseMean" class="gt_row gt_right">383.74</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">rfc4</td>
## <td headers="log2FoldChange" class="gt_row gt_right">1.60</td>
## <td headers="padj" class="gt_row gt_right">2.551 × 10<sup style='font-size: 65%;'>−10</sup></td>
## <td headers="baseMean" class="gt_row gt_right">296.30</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">ncapd3</td>
## <td headers="log2FoldChange" class="gt_row gt_right">2.49</td>
## <td headers="padj" class="gt_row gt_right">3.553 × 10<sup style='font-size: 65%;'>−10</sup></td>
## <td headers="baseMean" class="gt_row gt_right">225.60</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">smc2</td>
## <td headers="log2FoldChange" class="gt_row gt_right">2.16</td>
## <td headers="padj" class="gt_row gt_right">5.299 × 10<sup style='font-size: 65%;'>−10</sup></td>
## <td headers="baseMean" class="gt_row gt_right">410.25</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">zgc:194101</td>
## <td headers="log2FoldChange" class="gt_row gt_right">3.67</td>
## <td headers="padj" class="gt_row gt_right">9.834 × 10<sup style='font-size: 65%;'>−10</sup></td>
## <td headers="baseMean" class="gt_row gt_right">958.86</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">acp2</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−1.55</td>
## <td headers="padj" class="gt_row gt_right">1.194 × 10<sup style='font-size: 65%;'>−9</sup></td>
## <td headers="baseMean" class="gt_row gt_right">1,703.10</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">klhdc3</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−0.89</td>
## <td headers="padj" class="gt_row gt_right">1.194 × 10<sup style='font-size: 65%;'>−9</sup></td>
## <td headers="baseMean" class="gt_row gt_right">784.36</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">nup93</td>
## <td headers="log2FoldChange" class="gt_row gt_right">1.34</td>
## <td headers="padj" class="gt_row gt_right">1.242 × 10<sup style='font-size: 65%;'>−9</sup></td>
## <td headers="baseMean" class="gt_row gt_right">792.81</td></tr>
##   </tbody>
##   
##   
## </table>
## </div>

02) Historical Contingency Analysis

Sig Genes

Volcano Plots

Summary Table

summary_table

Historical Contingency Summary
Effect of prior stressors on parasite response
Treatment Comparison	Upregulated Genes	Downregulated Genes	Total Significant
ABX+PARA+ vs PARA+	26	23	49
TEMP+PARA+ vs PARA+	93	44	137
ABX+TEMP+PARA+ vs PARA+	5	13	18

Top Genes Tables

## ### Top 15 Significant Genes: A_plus_T_minus_P_plus_vs_A_minus_T_minus_P_plus 
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##       <td colspan="4" class="gt_heading gt_title gt_font_normal gt_bottom_border" style>Top 15 Significant Genes: A_plus_T_minus_P_plus_vs_A_minus_T_minus_P_plus</td>
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##     
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##       <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="Gene">Gene</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="log2 Fold Change">log2 Fold Change</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="Adjusted p-value">Adjusted p-value</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="Base Mean">Base Mean</th>
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##     <tr><td headers="gene" class="gt_row gt_left">LOC137490512</td>
## <td headers="log2FoldChange" class="gt_row gt_right">47.23</td>
## <td headers="padj" class="gt_row gt_right">2.104 × 10<sup style='font-size: 65%;'>−43</sup></td>
## <td headers="baseMean" class="gt_row gt_right">11.77</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">LOC141382111</td>
## <td headers="log2FoldChange" class="gt_row gt_right">34.16</td>
## <td headers="padj" class="gt_row gt_right">1.267 × 10<sup style='font-size: 65%;'>−14</sup></td>
## <td headers="baseMean" class="gt_row gt_right">7.24</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">LOC141374967</td>
## <td headers="log2FoldChange" class="gt_row gt_right">39.53</td>
## <td headers="padj" class="gt_row gt_right">7.357 × 10<sup style='font-size: 65%;'>−11</sup></td>
## <td headers="baseMean" class="gt_row gt_right">4.45</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">pvalb9</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−5.00</td>
## <td headers="padj" class="gt_row gt_right">4.066 × 10<sup style='font-size: 65%;'>−6</sup></td>
## <td headers="baseMean" class="gt_row gt_right">952.63</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">zgc:153738</td>
## <td headers="log2FoldChange" class="gt_row gt_right">3.66</td>
## <td headers="padj" class="gt_row gt_right">1.160 × 10<sup style='font-size: 65%;'>−5</sup></td>
## <td headers="baseMean" class="gt_row gt_right">38.40</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">zmp:0000000629</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−4.77</td>
## <td headers="padj" class="gt_row gt_right">9.427 × 10<sup style='font-size: 65%;'>−5</sup></td>
## <td headers="baseMean" class="gt_row gt_right">89.03</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">LOC137487415</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−2.23</td>
## <td headers="padj" class="gt_row gt_right">2.823 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">37.99</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">crp7</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−3.69</td>
## <td headers="padj" class="gt_row gt_right">9.502 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">91.28</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">itga2b</td>
## <td headers="log2FoldChange" class="gt_row gt_right">2.53</td>
## <td headers="padj" class="gt_row gt_right">1.329 × 10<sup style='font-size: 65%;'>−2</sup></td>
## <td headers="baseMean" class="gt_row gt_right">30.44</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">ugt5a4</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−2.35</td>
## <td headers="padj" class="gt_row gt_right">1.508 × 10<sup style='font-size: 65%;'>−2</sup></td>
## <td headers="baseMean" class="gt_row gt_right">696.32</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">LOC137487483</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−1.74</td>
## <td headers="padj" class="gt_row gt_right">1.816 × 10<sup style='font-size: 65%;'>−2</sup></td>
## <td headers="baseMean" class="gt_row gt_right">369.03</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">cspp1a</td>
## <td headers="log2FoldChange" class="gt_row gt_right">2.83</td>
## <td headers="padj" class="gt_row gt_right">2.256 × 10<sup style='font-size: 65%;'>−2</sup></td>
## <td headers="baseMean" class="gt_row gt_right">23.22</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">foxj1b</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−3.25</td>
## <td headers="padj" class="gt_row gt_right">2.487 × 10<sup style='font-size: 65%;'>−2</sup></td>
## <td headers="baseMean" class="gt_row gt_right">5.77</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">gatm</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−2.03</td>
## <td headers="padj" class="gt_row gt_right">2.487 × 10<sup style='font-size: 65%;'>−2</sup></td>
## <td headers="baseMean" class="gt_row gt_right">1,251.50</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">hydin</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−1.91</td>
## <td headers="padj" class="gt_row gt_right">2.487 × 10<sup style='font-size: 65%;'>−2</sup></td>
## <td headers="baseMean" class="gt_row gt_right">60.02</td></tr>
##   </tbody>
##   
##   
## </table>
## </div>
## 
## ### Top 15 Significant Genes: A_minus_T_plus_P_plus_vs_A_minus_T_minus_P_plus 
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##   <thead>
##     <tr class="gt_heading">
##       <td colspan="4" class="gt_heading gt_title gt_font_normal gt_bottom_border" style>Top 15 Significant Genes: A_minus_T_plus_P_plus_vs_A_minus_T_minus_P_plus</td>
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##     
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##       <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="Gene">Gene</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="log2 Fold Change">log2 Fold Change</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="Adjusted p-value">Adjusted p-value</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="Base Mean">Base Mean</th>
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##     <tr><td headers="gene" class="gt_row gt_left">LOC137490512</td>
## <td headers="log2FoldChange" class="gt_row gt_right">46.49</td>
## <td headers="padj" class="gt_row gt_right">5.864 × 10<sup style='font-size: 65%;'>−42</sup></td>
## <td headers="baseMean" class="gt_row gt_right">11.77</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">LOC141382111</td>
## <td headers="log2FoldChange" class="gt_row gt_right">37.01</td>
## <td headers="padj" class="gt_row gt_right">1.105 × 10<sup style='font-size: 65%;'>−17</sup></td>
## <td headers="baseMean" class="gt_row gt_right">7.24</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">LOC141374967</td>
## <td headers="log2FoldChange" class="gt_row gt_right">39.54</td>
## <td headers="padj" class="gt_row gt_right">7.311 × 10<sup style='font-size: 65%;'>−11</sup></td>
## <td headers="baseMean" class="gt_row gt_right">4.45</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">LOC141375690</td>
## <td headers="log2FoldChange" class="gt_row gt_right">30.75</td>
## <td headers="padj" class="gt_row gt_right">9.231 × 10<sup style='font-size: 65%;'>−6</sup></td>
## <td headers="baseMean" class="gt_row gt_right">10.73</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">lsm7</td>
## <td headers="log2FoldChange" class="gt_row gt_right">0.74</td>
## <td headers="padj" class="gt_row gt_right">7.724 × 10<sup style='font-size: 65%;'>−5</sup></td>
## <td headers="baseMean" class="gt_row gt_right">576.60</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">LOC137487415</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−2.51</td>
## <td headers="padj" class="gt_row gt_right">1.219 × 10<sup style='font-size: 65%;'>−4</sup></td>
## <td headers="baseMean" class="gt_row gt_right">37.99</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">slc26a3.1</td>
## <td headers="log2FoldChange" class="gt_row gt_right">3.84</td>
## <td headers="padj" class="gt_row gt_right">1.219 × 10<sup style='font-size: 65%;'>−4</sup></td>
## <td headers="baseMean" class="gt_row gt_right">186.97</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">hmgb2a</td>
## <td headers="log2FoldChange" class="gt_row gt_right">0.71</td>
## <td headers="padj" class="gt_row gt_right">4.169 × 10<sup style='font-size: 65%;'>−4</sup></td>
## <td headers="baseMean" class="gt_row gt_right">3,270.81</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">lsm8</td>
## <td headers="log2FoldChange" class="gt_row gt_right">0.70</td>
## <td headers="padj" class="gt_row gt_right">4.169 × 10<sup style='font-size: 65%;'>−4</sup></td>
## <td headers="baseMean" class="gt_row gt_right">255.36</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">si:ch211-194e1.7</td>
## <td headers="log2FoldChange" class="gt_row gt_right">23.03</td>
## <td headers="padj" class="gt_row gt_right">9.092 × 10<sup style='font-size: 65%;'>−4</sup></td>
## <td headers="baseMean" class="gt_row gt_right">13.99</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">cirbpa</td>
## <td headers="log2FoldChange" class="gt_row gt_right">0.65</td>
## <td headers="padj" class="gt_row gt_right">1.528 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">6,839.51</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">dut</td>
## <td headers="log2FoldChange" class="gt_row gt_right">1.10</td>
## <td headers="padj" class="gt_row gt_right">1.528 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">513.03</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">patj</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−0.58</td>
## <td headers="padj" class="gt_row gt_right">1.528 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">894.79</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">vrk1</td>
## <td headers="log2FoldChange" class="gt_row gt_right">0.80</td>
## <td headers="padj" class="gt_row gt_right">1.528 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">386.41</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">nedd4l</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−0.64</td>
## <td headers="padj" class="gt_row gt_right">1.630 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">1,081.30</td></tr>
##   </tbody>
##   
##   
## </table>
## </div>
## 
## ### Top 15 Significant Genes: A_plus_T_plus_P_plus_vs_A_minus_T_minus_P_plus 
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##       <td colspan="4" class="gt_heading gt_title gt_font_normal gt_bottom_border" style>Top 15 Significant Genes: A_plus_T_plus_P_plus_vs_A_minus_T_minus_P_plus</td>
##     </tr>
##     
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##       <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="Gene">Gene</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="log2 Fold Change">log2 Fold Change</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="Adjusted p-value">Adjusted p-value</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="Base Mean">Base Mean</th>
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##     <tr><td headers="gene" class="gt_row gt_left">LOC137490512</td>
## <td headers="log2FoldChange" class="gt_row gt_right">47.03</td>
## <td headers="padj" class="gt_row gt_right">5.365 × 10<sup style='font-size: 65%;'>−43</sup></td>
## <td headers="baseMean" class="gt_row gt_right">11.77</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">LOC141381096</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−41.69</td>
## <td headers="padj" class="gt_row gt_right">6.426 × 10<sup style='font-size: 65%;'>−26</sup></td>
## <td headers="baseMean" class="gt_row gt_right">19.89</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">LOC141375690</td>
## <td headers="log2FoldChange" class="gt_row gt_right">30.39</td>
## <td headers="padj" class="gt_row gt_right">1.902 × 10<sup style='font-size: 65%;'>−5</sup></td>
## <td headers="baseMean" class="gt_row gt_right">10.73</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">zmp:0000000629</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−5.02</td>
## <td headers="padj" class="gt_row gt_right">2.690 × 10<sup style='font-size: 65%;'>−5</sup></td>
## <td headers="baseMean" class="gt_row gt_right">89.03</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">pvalb9</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−4.02</td>
## <td headers="padj" class="gt_row gt_right">2.994 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">952.63</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">si:ch211-194e1.7</td>
## <td headers="log2FoldChange" class="gt_row gt_right">22.43</td>
## <td headers="padj" class="gt_row gt_right">2.994 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">13.99</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">celsr1b</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−3.14</td>
## <td headers="padj" class="gt_row gt_right">6.729 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">41.85</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">zp3d.1</td>
## <td headers="log2FoldChange" class="gt_row gt_right">3.22</td>
## <td headers="padj" class="gt_row gt_right">9.539 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">28.16</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">hydin</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−2.02</td>
## <td headers="padj" class="gt_row gt_right">1.368 × 10<sup style='font-size: 65%;'>−2</sup></td>
## <td headers="baseMean" class="gt_row gt_right">60.02</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">igsf21b</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−3.99</td>
## <td headers="padj" class="gt_row gt_right">1.499 × 10<sup style='font-size: 65%;'>−2</sup></td>
## <td headers="baseMean" class="gt_row gt_right">43.32</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">ifi27.6</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−2.46</td>
## <td headers="padj" class="gt_row gt_right">1.564 × 10<sup style='font-size: 65%;'>−2</sup></td>
## <td headers="baseMean" class="gt_row gt_right">610.65</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">LOC141379879</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−5.72</td>
## <td headers="padj" class="gt_row gt_right">1.564 × 10<sup style='font-size: 65%;'>−2</sup></td>
## <td headers="baseMean" class="gt_row gt_right">99.05</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">ckmb</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−4.54</td>
## <td headers="padj" class="gt_row gt_right">1.970 × 10<sup style='font-size: 65%;'>−2</sup></td>
## <td headers="baseMean" class="gt_row gt_right">52.80</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">slc4a5b</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−4.16</td>
## <td headers="padj" class="gt_row gt_right">3.315 × 10<sup style='font-size: 65%;'>−2</sup></td>
## <td headers="baseMean" class="gt_row gt_right">342.17</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">abhd2a</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−0.92</td>
## <td headers="padj" class="gt_row gt_right">4.860 × 10<sup style='font-size: 65%;'>−2</sup></td>
## <td headers="baseMean" class="gt_row gt_right">580.64</td></tr>
##   </tbody>
##   
##   
## </table>
## </div>

03) Recovery Analysis

Sig Genes

Volcano Plots

Summary Table

summary_table

Recovery Analysis Summary
Effect of prior stressors on recovery
Treatment Comparison	Upregulated Genes	Downregulated Genes	Total Significant
ABX+ vs Control	8	27	35
TEMP+ vs Control	6	41	47
ABX+TEMP+ vs Control	18	99	117

Top Genes Tables

## ### Top 15 Significant Genes: A_plus_T_minus_P_minus_vs_A_minus_T_minus_P_minus 
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## </style>
##   <table class="gt_table" data-quarto-disable-processing="false" data-quarto-bootstrap="false">
##   <thead>
##     <tr class="gt_heading">
##       <td colspan="4" class="gt_heading gt_title gt_font_normal gt_bottom_border" style>Top 15 Significant Genes: A_plus_T_minus_P_minus_vs_A_minus_T_minus_P_minus</td>
##     </tr>
##     
##     <tr class="gt_col_headings">
##       <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="Gene">Gene</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="log2 Fold Change">log2 Fold Change</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="Adjusted p-value">Adjusted p-value</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="Base Mean">Base Mean</th>
##     </tr>
##   </thead>
##   <tbody class="gt_table_body">
##     <tr><td headers="gene" class="gt_row gt_left">LOC100147849</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−19.67</td>
## <td headers="padj" class="gt_row gt_right">8.847 × 10<sup style='font-size: 65%;'>−22</sup></td>
## <td headers="baseMean" class="gt_row gt_right">17.11</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">si:ch211-125e6.14</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−24.55</td>
## <td headers="padj" class="gt_row gt_right">3.610 × 10<sup style='font-size: 65%;'>−14</sup></td>
## <td headers="baseMean" class="gt_row gt_right">728.43</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">ncoa7a</td>
## <td headers="log2FoldChange" class="gt_row gt_right">3.39</td>
## <td headers="padj" class="gt_row gt_right">4.678 × 10<sup style='font-size: 65%;'>−6</sup></td>
## <td headers="baseMean" class="gt_row gt_right">672.56</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">LOC103909395</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−16.57</td>
## <td headers="padj" class="gt_row gt_right">4.354 × 10<sup style='font-size: 65%;'>−5</sup></td>
## <td headers="baseMean" class="gt_row gt_right">6.21</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">LOC110438438</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−9.78</td>
## <td headers="padj" class="gt_row gt_right">2.514 × 10<sup style='font-size: 65%;'>−4</sup></td>
## <td headers="baseMean" class="gt_row gt_right">159.54</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">LOC137491340</td>
## <td headers="log2FoldChange" class="gt_row gt_right">19.19</td>
## <td headers="padj" class="gt_row gt_right">4.002 × 10<sup style='font-size: 65%;'>−4</sup></td>
## <td headers="baseMean" class="gt_row gt_right">12.62</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">LOC101882847</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−6.61</td>
## <td headers="padj" class="gt_row gt_right">5.176 × 10<sup style='font-size: 65%;'>−4</sup></td>
## <td headers="baseMean" class="gt_row gt_right">114.36</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">LOC141379337</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−9.32</td>
## <td headers="padj" class="gt_row gt_right">1.265 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">69.70</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">LOC141379345</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−9.97</td>
## <td headers="padj" class="gt_row gt_right">1.569 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">48.08</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">LOC141379342</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−5.80</td>
## <td headers="padj" class="gt_row gt_right">2.578 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">40.33</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">pla2g3</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−4.77</td>
## <td headers="padj" class="gt_row gt_right">2.638 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">143.64</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">ccl35.1</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−3.47</td>
## <td headers="padj" class="gt_row gt_right">5.820 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">65.26</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">si:dkey-3k24.8</td>
## <td headers="log2FoldChange" class="gt_row gt_right">3.16</td>
## <td headers="padj" class="gt_row gt_right">6.386 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">112.79</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">ankrd66</td>
## <td headers="log2FoldChange" class="gt_row gt_right">18.08</td>
## <td headers="padj" class="gt_row gt_right">8.219 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">4.74</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">LOC137487211</td>
## <td headers="log2FoldChange" class="gt_row gt_right">2.71</td>
## <td headers="padj" class="gt_row gt_right">1.279 × 10<sup style='font-size: 65%;'>−2</sup></td>
## <td headers="baseMean" class="gt_row gt_right">36.37</td></tr>
##   </tbody>
##   
##   
## </table>
## </div>
## 
## ### Top 15 Significant Genes: A_minus_T_plus_P_minus_vs_A_minus_T_minus_P_minus 
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##   <table class="gt_table" data-quarto-disable-processing="false" data-quarto-bootstrap="false">
##   <thead>
##     <tr class="gt_heading">
##       <td colspan="4" class="gt_heading gt_title gt_font_normal gt_bottom_border" style>Top 15 Significant Genes: A_minus_T_plus_P_minus_vs_A_minus_T_minus_P_minus</td>
##     </tr>
##     
##     <tr class="gt_col_headings">
##       <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="Gene">Gene</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="log2 Fold Change">log2 Fold Change</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="Adjusted p-value">Adjusted p-value</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="Base Mean">Base Mean</th>
##     </tr>
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##   <tbody class="gt_table_body">
##     <tr><td headers="gene" class="gt_row gt_left">LOC137487668</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−23.06</td>
## <td headers="padj" class="gt_row gt_right">1.472 × 10<sup style='font-size: 65%;'>−11</sup></td>
## <td headers="baseMean" class="gt_row gt_right">17.22</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">cpdb</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−18.35</td>
## <td headers="padj" class="gt_row gt_right">2.208 × 10<sup style='font-size: 65%;'>−9</sup></td>
## <td headers="baseMean" class="gt_row gt_right">10.44</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">LOC141381605</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−23.61</td>
## <td headers="padj" class="gt_row gt_right">2.209 × 10<sup style='font-size: 65%;'>−4</sup></td>
## <td headers="baseMean" class="gt_row gt_right">29.88</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">lhx8a</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−17.40</td>
## <td headers="padj" class="gt_row gt_right">5.190 × 10<sup style='font-size: 65%;'>−4</sup></td>
## <td headers="baseMean" class="gt_row gt_right">5.45</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">nots</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−8.89</td>
## <td headers="padj" class="gt_row gt_right">5.190 × 10<sup style='font-size: 65%;'>−4</sup></td>
## <td headers="baseMean" class="gt_row gt_right">4,683.87</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">LOC137491340</td>
## <td headers="log2FoldChange" class="gt_row gt_right">18.83</td>
## <td headers="padj" class="gt_row gt_right">6.818 × 10<sup style='font-size: 65%;'>−4</sup></td>
## <td headers="baseMean" class="gt_row gt_right">12.62</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">vtg5</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−8.78</td>
## <td headers="padj" class="gt_row gt_right">7.009 × 10<sup style='font-size: 65%;'>−4</sup></td>
## <td headers="baseMean" class="gt_row gt_right">206,858.02</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">rcn3</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−4.67</td>
## <td headers="padj" class="gt_row gt_right">1.652 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">1,094.80</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">rtn1a</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−3.83</td>
## <td headers="padj" class="gt_row gt_right">2.503 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">2,599.05</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">mthfr</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−2.61</td>
## <td headers="padj" class="gt_row gt_right">3.492 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">364.46</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">mboat2a</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−2.08</td>
## <td headers="padj" class="gt_row gt_right">3.788 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">222.02</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">slc43a1a</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−2.34</td>
## <td headers="padj" class="gt_row gt_right">3.788 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">246.46</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">slc7a1b</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−2.05</td>
## <td headers="padj" class="gt_row gt_right">3.788 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">173.73</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">vtg7</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−9.38</td>
## <td headers="padj" class="gt_row gt_right">3.788 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">141,150.32</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">vtg8</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−6.25</td>
## <td headers="padj" class="gt_row gt_right">3.788 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">134.46</td></tr>
##   </tbody>
##   
##   
## </table>
## </div>
## 
## ### Top 15 Significant Genes: A_plus_T_plus_P_minus_vs_A_minus_T_minus_P_minus 
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##       <td colspan="4" class="gt_heading gt_title gt_font_normal gt_bottom_border" style>Top 15 Significant Genes: A_plus_T_plus_P_minus_vs_A_minus_T_minus_P_minus</td>
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##     
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##       <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="Gene">Gene</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="log2 Fold Change">log2 Fold Change</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="Adjusted p-value">Adjusted p-value</th>
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##     <tr><td headers="gene" class="gt_row gt_left">LOC101885452</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−21.14</td>
## <td headers="padj" class="gt_row gt_right">1.759 × 10<sup style='font-size: 65%;'>−27</sup></td>
## <td headers="baseMean" class="gt_row gt_right">27.72</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">LOC101887118</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−19.26</td>
## <td headers="padj" class="gt_row gt_right">1.655 × 10<sup style='font-size: 65%;'>−11</sup></td>
## <td headers="baseMean" class="gt_row gt_right">8.03</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">mhc2dgb</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−26.07</td>
## <td headers="padj" class="gt_row gt_right">4.051 × 10<sup style='font-size: 65%;'>−7</sup></td>
## <td headers="baseMean" class="gt_row gt_right">256.45</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">LOC137495296</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−10.77</td>
## <td headers="padj" class="gt_row gt_right">8.250 × 10<sup style='font-size: 65%;'>−5</sup></td>
## <td headers="baseMean" class="gt_row gt_right">226.20</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">LOC137491340</td>
## <td headers="log2FoldChange" class="gt_row gt_right">19.55</td>
## <td headers="padj" class="gt_row gt_right">2.767 × 10<sup style='font-size: 65%;'>−4</sup></td>
## <td headers="baseMean" class="gt_row gt_right">12.62</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">LOC101882702</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−4.80</td>
## <td headers="padj" class="gt_row gt_right">4.937 × 10<sup style='font-size: 65%;'>−4</sup></td>
## <td headers="baseMean" class="gt_row gt_right">378.81</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">si:dkey-211g8.5</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−3.74</td>
## <td headers="padj" class="gt_row gt_right">5.647 × 10<sup style='font-size: 65%;'>−4</sup></td>
## <td headers="baseMean" class="gt_row gt_right">198.63</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">ly6m5</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−4.64</td>
## <td headers="padj" class="gt_row gt_right">6.740 × 10<sup style='font-size: 65%;'>−4</sup></td>
## <td headers="baseMean" class="gt_row gt_right">279.80</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">pld4</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−3.03</td>
## <td headers="padj" class="gt_row gt_right">1.180 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">132.58</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">stat1b</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−2.73</td>
## <td headers="padj" class="gt_row gt_right">1.293 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">2,635.38</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">ftr11</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−2.49</td>
## <td headers="padj" class="gt_row gt_right">1.620 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">142.87</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">LOC100001589</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−2.38</td>
## <td headers="padj" class="gt_row gt_right">1.620 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">553.61</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">mxa</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−2.66</td>
## <td headers="padj" class="gt_row gt_right">1.620 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">305.17</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">si:ch211-217k17.11</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−2.66</td>
## <td headers="padj" class="gt_row gt_right">1.620 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">6,447.32</td></tr>
##     <tr><td headers="gene" class="gt_row gt_left">si:ch211-271e10.3</td>
## <td headers="log2FoldChange" class="gt_row gt_right">−2.87</td>
## <td headers="padj" class="gt_row gt_right">1.620 × 10<sup style='font-size: 65%;'>−3</sup></td>
## <td headers="baseMean" class="gt_row gt_right">2,015.31</td></tr>
##   </tbody>
##   
##   
## </table>
## </div>

Enrichment Analysis

Setup and Run Enrichment Analysis

# Set up parallel processing for enrichment analysis
plan(multisession, workers = min(4, availableCores()))

# Run enrichment analysis for all three analyses
enrichment_results <- list()

for (analysis_name in names(all_results)) {
  cat("\n=== Processing enrichment for:", analysis_name, "===\n")
  
  # Check if we have results for this analysis
  if (!is.null(all_results[[analysis_name]])) {
    enrichment_results[[analysis_name]] <- run_enrichment_analysis(analysis_name, all_results[[analysis_name]])
  } else {
    cat("No results available for:", analysis_name, "\n")
  }
}

## 
## === Processing enrichment for: All_Treatments ===
## 
## === Running Enrichment Analysis for: All_Treatments ===

## 'select()' returned 1:many mapping between keys and columns

## 'select()' returned 1:1 mapping between keys and columns

## 'select()' returned 1:many mapping between keys and columns

## 'select()' returned 1:1 mapping between keys and columns

## 'select()' returned 1:many mapping between keys and columns

## 'select()' returned 1:1 mapping between keys and columns

## 'select()' returned 1:many mapping between keys and columns

## Running GO enrichment...
## Performing GO enrichment for: A_minus_T_minus_P_plus_vs_A_minus_T_minus_P_minus 
## Number of genes: 1578

## 'select()' returned 1:1 mapping between keys and columns

## Performing GO enrichment for: A_plus_T_minus_P_minus_vs_A_minus_T_minus_P_minus 
## Number of genes: 23

## 'select()' returned 1:1 mapping between keys and columns

## Performing GO enrichment for: A_plus_T_minus_P_plus_vs_A_minus_T_minus_P_minus 
## Number of genes: 3076

## 'select()' returned 1:1 mapping between keys and columns

## Performing GO enrichment for: A_minus_T_plus_P_minus_vs_A_minus_T_minus_P_minus 
## Number of genes: 38

## 'select()' returned 1:1 mapping between keys and columns

## Performing GO enrichment for: A_minus_T_plus_P_plus_vs_A_minus_T_minus_P_minus 
## Number of genes: 2882

## 'select()' returned 1:1 mapping between keys and columns

## Performing GO enrichment for: A_plus_T_plus_P_minus_vs_A_minus_T_minus_P_minus 
## Number of genes: 89

## 'select()' returned 1:1 mapping between keys and columns

## Performing GO enrichment for: A_plus_T_plus_P_plus_vs_A_minus_T_minus_P_minus 
## Number of genes: 2242

## 'select()' returned 1:1 mapping between keys and columns

## Running KEGG enrichment...
## Performing KEGG enrichment for: A_minus_T_minus_P_plus_vs_A_minus_T_minus_P_minus 
## Number of genes: 1578

## Reading KEGG annotation online: "https://rest.kegg.jp/link/dre/pathway"...

## Reading KEGG annotation online: "https://rest.kegg.jp/list/pathway/dre"...

## Reading KEGG annotation online: "https://rest.kegg.jp/conv/ncbi-geneid/dre"...

## Performing KEGG enrichment for: A_plus_T_minus_P_minus_vs_A_minus_T_minus_P_minus 
## Number of genes: 23 
## Performing KEGG enrichment for: A_plus_T_minus_P_plus_vs_A_minus_T_minus_P_minus 
## Number of genes: 3076 
## Performing KEGG enrichment for: A_minus_T_plus_P_minus_vs_A_minus_T_minus_P_minus 
## Number of genes: 38 
## Performing KEGG enrichment for: A_minus_T_plus_P_plus_vs_A_minus_T_minus_P_minus 
## Number of genes: 2882 
## Performing KEGG enrichment for: A_plus_T_plus_P_minus_vs_A_minus_T_minus_P_minus 
## Number of genes: 89 
## Performing KEGG enrichment for: A_plus_T_plus_P_plus_vs_A_minus_T_minus_P_minus 
## Number of genes: 2242 
## 
## === Processing enrichment for: Parasite_Effect ===
## 
## === Running Enrichment Analysis for: Parasite_Effect ===

## 'select()' returned 1:many mapping between keys and columns

## Running GO enrichment...
## Performing GO enrichment for: A_minus_T_minus_P_plus_vs_A_minus_T_minus_P_minus 
## Number of genes: 1578

## 'select()' returned 1:1 mapping between keys and columns

## Running KEGG enrichment...
## Performing KEGG enrichment for: A_minus_T_minus_P_plus_vs_A_minus_T_minus_P_minus 
## Number of genes: 1578 
## 
## === Processing enrichment for: Historical_Contingency ===
## 
## === Running Enrichment Analysis for: Historical_Contingency ===

## 'select()' returned 1:1 mapping between keys and columns

## 'select()' returned 1:1 mapping between keys and columns
## 'select()' returned 1:1 mapping between keys and columns

## Running GO enrichment...
## Performing GO enrichment for: A_plus_T_minus_P_plus_vs_A_minus_T_minus_P_plus 
## Number of genes: 36

## 'select()' returned 1:1 mapping between keys and columns

## Performing GO enrichment for: A_minus_T_plus_P_plus_vs_A_minus_T_minus_P_plus 
## Number of genes: 51

## 'select()' returned 1:1 mapping between keys and columns

## Performing GO enrichment for: A_plus_T_plus_P_plus_vs_A_minus_T_minus_P_plus 
## Number of genes: 13

## 'select()' returned 1:1 mapping between keys and columns

## Running KEGG enrichment...
## Performing KEGG enrichment for: A_plus_T_minus_P_plus_vs_A_minus_T_minus_P_plus 
## Number of genes: 36 
## Performing KEGG enrichment for: A_minus_T_plus_P_plus_vs_A_minus_T_minus_P_plus 
## Number of genes: 51 
## Performing KEGG enrichment for: A_plus_T_plus_P_plus_vs_A_minus_T_minus_P_plus 
## Number of genes: 13 
## 
## === Processing enrichment for: Recovery_Analysis ===
## 
## === Running Enrichment Analysis for: Recovery_Analysis ===

## 'select()' returned 1:1 mapping between keys and columns
## 'select()' returned 1:1 mapping between keys and columns
## 'select()' returned 1:1 mapping between keys and columns

## Running GO enrichment...
## Performing GO enrichment for: A_plus_T_minus_P_minus_vs_A_minus_T_minus_P_minus 
## Number of genes: 23

## 'select()' returned 1:1 mapping between keys and columns

## Performing GO enrichment for: A_minus_T_plus_P_minus_vs_A_minus_T_minus_P_minus 
## Number of genes: 38

## 'select()' returned 1:1 mapping between keys and columns

## Performing GO enrichment for: A_plus_T_plus_P_minus_vs_A_minus_T_minus_P_minus 
## Number of genes: 89

## 'select()' returned 1:1 mapping between keys and columns

## Running KEGG enrichment...
## Performing KEGG enrichment for: A_plus_T_minus_P_minus_vs_A_minus_T_minus_P_minus 
## Number of genes: 23 
## Performing KEGG enrichment for: A_minus_T_plus_P_minus_vs_A_minus_T_minus_P_minus 
## Number of genes: 38 
## Performing KEGG enrichment for: A_plus_T_plus_P_minus_vs_A_minus_T_minus_P_minus 
## Number of genes: 89

# Clean up parallel processing
plan(sequential)

cat("\n=== Enrichment Analysis Complete ===\n")

## 
## === Enrichment Analysis Complete ===

00) All Treatments Analysis

01) Parasite Effect Analysis

02) Historical Contingency Analysis

03) Recovery Analysis

Summary Tables

## 
## === Processing All_Treatments ===
## 
## === Processing Parasite_Effect ===
## 
## === Processing Historical_Contingency ===
## 
## === Processing Recovery_Analysis ===
## 
## ## All_Treatments Enrichment Summary
## 
## ### Top GO Terms
## 
## ### Top KEGG Pathways
## 
## ---
## 
## ## Parasite_Effect Enrichment Summary
## 
## ### Top GO Terms
## 
## ### Top KEGG Pathways
## 
## ---
## 
## ## Historical_Contingency Enrichment Summary
## 
## ### Top GO Terms
## 
## ### Top KEGG Pathways
## 
## ---
## 
## ## Recovery_Analysis Enrichment Summary
## 
## ### Top GO Terms
## 
## ### Top KEGG Pathways
## 
## ---
## 
## ## Combined Summary Across All Analyses
## 
## ### Combined GO Terms Summary
## 
## ### Combined KEGG Pathways Summary

## $All_Treatments_GO
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##   <table class="gt_table" data-quarto-disable-processing="false" data-quarto-bootstrap="false">
##   <thead>
##     <tr class="gt_heading">
##       <td colspan="5" class="gt_heading gt_title gt_font_normal" style>Top GO Terms - All_Treatments</td>
##     </tr>
##     <tr class="gt_heading">
##       <td colspan="5" class="gt_heading gt_subtitle gt_font_normal gt_bottom_border" style>Biological Process enrichment (top 10 per contrast)</td>
##     </tr>
##     <tr class="gt_col_headings">
##       <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="Treatment Comparison">Treatment Comparison</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="GO Term">GO Term</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="-log10(adj p-value)">-log10(adj p-value)</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="Gene Count">Gene Count</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="Mean log2FC">Mean log2FC</th>
##     </tr>
##   </thead>
##   <tbody class="gt_table_body">
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">43.746</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">82</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.963</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">mitotic cell cycle process</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">35.875</td>
## <td headers="Count" class="gt_row gt_right gt_striped">114</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.204</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">DNA-templated DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">33.442</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">56</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.020</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">chromosome organization</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">31.704</td>
## <td headers="Count" class="gt_row gt_right gt_striped">94</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.083</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">chromosome segregation</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">31.165</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">79</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.272</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">nuclear division</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">28.063</td>
## <td headers="Count" class="gt_row gt_right gt_striped">72</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.269</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">DNA repair</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">27.219</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">104</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.964</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">DNA damage response</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">27.194</td>
## <td headers="Count" class="gt_row gt_right gt_striped">122</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.901</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">nuclear chromosome segregation</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">25.738</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">56</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.292</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">organelle fission</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">25.633</td>
## <td headers="Count" class="gt_row gt_right gt_striped">74</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.219</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">defense response</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">8.202</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">13</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.390</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to virus</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">8.202</td>
## <td headers="Count" class="gt_row gt_right gt_striped">8</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.820</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">defense response to other organism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">7.622</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">11</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.700</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to biotic stimulus</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">7.622</td>
## <td headers="Count" class="gt_row gt_right gt_striped">12</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.653</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">response to external biotic stimulus</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">7.622</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">12</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.653</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to other organism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">7.622</td>
## <td headers="Count" class="gt_row gt_right gt_striped">12</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.653</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">defense response to symbiont</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">5.901</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">6</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.735</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">defense response to virus</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">5.901</td>
## <td headers="Count" class="gt_row gt_right gt_striped">6</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.735</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">cytokine-mediated signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.734</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">4</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.223</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">cellular response to cytokine stimulus</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.700</td>
## <td headers="Count" class="gt_row gt_right gt_striped">4</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.223</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">36.497</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">85</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.148</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">chromosome segregation</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">32.107</td>
## <td headers="Count" class="gt_row gt_right gt_striped">92</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.423</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">DNA repair</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">31.115</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">129</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.005</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">DNA-templated DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">31.074</td>
## <td headers="Count" class="gt_row gt_right gt_striped">60</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.136</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">DNA damage response</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">30.391</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">151</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.930</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">mitotic cell cycle process</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">30.295</td>
## <td headers="Count" class="gt_row gt_right gt_striped">124</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.368</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">chromosome organization</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">27.626</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">103</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.307</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">nuclear division</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">26.108</td>
## <td headers="Count" class="gt_row gt_right gt_striped">80</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.535</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">nuclear chromosome segregation</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">24.428</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">62</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.532</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">organelle fission</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">23.724</td>
## <td headers="Count" class="gt_row gt_right gt_striped">83</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.440</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">cellular response to chemokine</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.795</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">chemokine-mediated signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.795</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">response to chemokine</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.795</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">granulocyte chemotaxis</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.526</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">neutrophil chemotaxis</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.526</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">granulocyte migration</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.523</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">leukocyte chemotaxis</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.523</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">neutrophil migration</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.523</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">L-phenylalanine catabolic process</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.871</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">L-phenylalanine metabolic process</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.871</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">alpha-amino acid metabolic process</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−1.070</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">amino acid metabolic process</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.070</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">antimicrobial humoral immune response mediated by antimicrobial peptide</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.340</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">arachidonate transport</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.772</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">arachidonic acid secretion</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.772</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">carboxylic acid transport</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−3.378</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">cell chemotaxis</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">cellular response to cytokine stimulus</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">chemotaxis</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">cytokine-mediated signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">endothelial to hematopoietic transition</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.754</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">erythrose 4-phosphate/phosphoenolpyruvate family amino acid catabolic process</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.871</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">erythrose 4-phosphate/phosphoenolpyruvate family amino acid metabolic process</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.871</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">icosanoid secretion</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.772</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">icosanoid transport</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.772</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">inflammatory response</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">leukocyte migration</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">myeloid leukocyte migration</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">organic acid transport</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−3.378</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">organic anion transport</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−3.378</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">polyamine metabolic process</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.730</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">positive regulation of wound healing</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.754</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">regulation of blood coagulation</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.754</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">regulation of hemostasis</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.754</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">regulation of neural retina development</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−3.621</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to cytokine</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">taxis</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">tyrosine metabolic process</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.871</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">41.099</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">88</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.140</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">DNA repair</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">40.741</td>
## <td headers="Count" class="gt_row gt_right gt_striped">140</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.898</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">DNA damage response</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">37.952</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">160</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.848</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">DNA-templated DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">35.898</td>
## <td headers="Count" class="gt_row gt_right gt_striped">63</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.153</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">chromosome segregation</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">33.055</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">91</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.647</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">chromosome organization</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">32.854</td>
## <td headers="Count" class="gt_row gt_right gt_striped">108</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.362</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">mitotic cell cycle process</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">30.759</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">122</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.402</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">nuclear division</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">27.337</td>
## <td headers="Count" class="gt_row gt_right gt_striped">80</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.561</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">organelle fission</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">25.691</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">84</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.425</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">nuclear chromosome segregation</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">25.468</td>
## <td headers="Count" class="gt_row gt_right gt_striped">62</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.739</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">cellular response to estrogen stimulus</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">11.573</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−9.231</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to estrogen</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">11.573</td>
## <td headers="Count" class="gt_row gt_right gt_striped">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−9.231</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">response to estradiol</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">11.015</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">6</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−9.270</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to lipid</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">6.552</td>
## <td headers="Count" class="gt_row gt_right gt_striped">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−8.304</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">cellular response to hormone stimulus</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">6.376</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−9.231</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">lipid transport</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">5.844</td>
## <td headers="Count" class="gt_row gt_right gt_striped">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−8.837</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">response to hormone</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">5.844</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−9.231</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to organic cyclic compound</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">5.812</td>
## <td headers="Count" class="gt_row gt_right gt_striped">6</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−9.270</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">lipid localization</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">5.777</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−8.837</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to oxygen-containing compound</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">4.495</td>
## <td headers="Count" class="gt_row gt_right gt_striped">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−8.304</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">chromosome segregation</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">36.852</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">74</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.983</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">36.170</td>
## <td headers="Count" class="gt_row gt_right gt_striped">65</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.703</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">mitotic cell cycle process</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">36.170</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">96</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.900</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">nuclear chromosome segregation</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">29.184</td>
## <td headers="Count" class="gt_row gt_right gt_striped">52</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.031</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">chromosome organization</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">28.831</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">76</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.837</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">nuclear division</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">27.500</td>
## <td headers="Count" class="gt_row gt_right gt_striped">61</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.946</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">sister chromatid segregation</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">26.900</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">43</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.978</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">organelle fission</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">25.799</td>
## <td headers="Count" class="gt_row gt_right gt_striped">63</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.895</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">DNA-templated DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">25.586</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">43</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.777</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">mitotic sister chromatid segregation</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">23.570</td>
## <td headers="Count" class="gt_row gt_right gt_striped">38</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.047</td></tr>
##   </tbody>
##   
##   
## </table>
## </div>
## 
## $All_Treatments_KEGG
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##   <table class="gt_table" data-quarto-disable-processing="false" data-quarto-bootstrap="false">
##   <thead>
##     <tr class="gt_heading">
##       <td colspan="5" class="gt_heading gt_title gt_font_normal" style>Top KEGG Pathways - All_Treatments</td>
##     </tr>
##     <tr class="gt_heading">
##       <td colspan="5" class="gt_heading gt_subtitle gt_font_normal gt_bottom_border" style>Pathway enrichment (top 10 per contrast)</td>
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##     <tr class="gt_col_headings">
##       <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="Treatment Comparison">Treatment Comparison</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="KEGG Pathway">KEGG Pathway</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="-log10(adj p-value)">-log10(adj p-value)</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="Gene Count">Gene Count</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="Mean log2FC">Mean log2FC</th>
##     </tr>
##   </thead>
##   <tbody class="gt_table_body">
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">26.277</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">30</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.993</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Cell cycle</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">26.007</td>
## <td headers="Count" class="gt_row gt_right gt_striped">63</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.012</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Mismatch repair</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">14.304</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">17</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.748</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Homologous recombination</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">14.148</td>
## <td headers="Count" class="gt_row gt_right gt_striped">22</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.889</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Fanconi anemia pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">9.354</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">20</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.078</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">PPAR signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">8.502</td>
## <td headers="Count" class="gt_row gt_right gt_striped">26</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.268</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Base excision repair</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">6.112</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">16</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.792</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">FoxO signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">5.928</td>
## <td headers="Count" class="gt_row gt_right gt_striped">33</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−0.250</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Nucleotide excision repair</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">5.625</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">17</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.775</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Apoptosis</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">5.402</td>
## <td headers="Count" class="gt_row gt_right gt_striped">34</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">0.474</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">p53 signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">5.402</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">21</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">0.495</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">NOD-like receptor signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">3.914</td>
## <td headers="Count" class="gt_row gt_right gt_striped">5</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.313</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">RIG-I-like receptor signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">3.914</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">4</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.309</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Herpes simplex virus 1 infection</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">3.777</td>
## <td headers="Count" class="gt_row gt_right gt_striped">5</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−7.243</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Toll-like receptor signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">3.605</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">4</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.535</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Apoptosis</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.526</td>
## <td headers="Count" class="gt_row gt_right gt_striped">3</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.431</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Cytokine-cytokine receptor interaction</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.526</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">3</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−1.422</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Cytosolic DNA-sensing pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.526</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.699</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">C-type lectin receptor signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.049</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−3.372</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Cell cycle</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">26.135</td>
## <td headers="Count" class="gt_row gt_right gt_striped">73</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.270</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">22.544</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">30</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.015</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Mismatch repair</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">15.314</td>
## <td headers="Count" class="gt_row gt_right gt_striped">19</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.882</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Homologous recombination</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">13.636</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">24</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.036</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Fanconi anemia pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">12.606</td>
## <td headers="Count" class="gt_row gt_right gt_striped">26</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.121</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Drug metabolism - other enzymes</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">7.972</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">32</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−0.879</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">PPAR signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">7.673</td>
## <td headers="Count" class="gt_row gt_right gt_striped">29</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.527</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Base excision repair</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">7.507</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">20</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.782</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Drug metabolism - cytochrome P450</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">6.812</td>
## <td headers="Count" class="gt_row gt_right gt_striped">24</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.723</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Retinol metabolism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">5.872</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">26</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−1.511</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Linoleic acid metabolism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.262</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.772</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Phenylalanine metabolism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.262</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.871</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Primary bile acid biosynthesis</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.262</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.270</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Ubiquinone and other terpenoid-quinone biosynthesis</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.262</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.871</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">alpha-Linolenic acid metabolism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.262</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.772</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Arachidonic acid metabolism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.226</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.772</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Arginine and proline metabolism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.226</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.730</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Cysteine and methionine metabolism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.226</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.871</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Ether lipid metabolism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.226</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.772</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Glutathione metabolism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.226</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.730</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Tyrosine metabolism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.226</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.871</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">28.698</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">34</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.996</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Cell cycle</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">27.177</td>
## <td headers="Count" class="gt_row gt_right gt_striped">75</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.317</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Homologous recombination</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">14.390</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">25</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.161</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Mismatch repair</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">13.479</td>
## <td headers="Count" class="gt_row gt_right gt_striped">18</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.039</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Fanconi anemia pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">13.309</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">27</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.180</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Base excision repair</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">12.892</td>
## <td headers="Count" class="gt_row gt_right gt_striped">26</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.610</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">PPAR signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">12.527</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">36</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−1.403</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Proteasome</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">8.327</td>
## <td headers="Count" class="gt_row gt_right gt_striped">23</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.305</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Nucleotide excision repair</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">7.055</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">22</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.758</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Apoptosis</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">6.211</td>
## <td headers="Count" class="gt_row gt_right gt_striped">44</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">0.543</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">FoxO signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">6.211</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">41</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">0.010</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Glycerolipid metabolism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.877</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.896</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Glycerophospholipid metabolism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.776</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−1.896</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Folate transport and metabolism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.222</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.609</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Protein export</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.222</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−1.277</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">RNA polymerase</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.222</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.415</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">One carbon pool by folate</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.213</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.609</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Cytosolic DNA-sensing pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.078</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.415</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Cell cycle</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">25.694</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">54</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.848</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">20.877</td>
## <td headers="Count" class="gt_row gt_right gt_striped">24</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.671</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Mismatch repair</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">8.846</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">12</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.708</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Homologous recombination</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">7.418</td>
## <td headers="Count" class="gt_row gt_right gt_striped">14</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.756</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Fanconi anemia pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">6.917</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">15</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.918</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">PPAR signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">5.354</td>
## <td headers="Count" class="gt_row gt_right gt_striped">18</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.483</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Nucleotide excision repair</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">5.151</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">14</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.554</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">FoxO signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">4.314</td>
## <td headers="Count" class="gt_row gt_right gt_striped">24</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−0.288</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">p53 signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">4.265</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">16</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">0.420</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Base excision repair</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">3.862</td>
## <td headers="Count" class="gt_row gt_right gt_striped">11</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.612</td></tr>
##   </tbody>
##   
##   
## </table>
## </div>
## 
## $Parasite_Effect_GO
## <div id="ciydemetbh" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
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##     <tr class="gt_heading">
##       <td colspan="5" class="gt_heading gt_title gt_font_normal" style>Top GO Terms - Parasite_Effect</td>
##     </tr>
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##       <td colspan="5" class="gt_heading gt_subtitle gt_font_normal gt_bottom_border" style>Biological Process enrichment (top 10 per contrast)</td>
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##       <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="Treatment Comparison">Treatment Comparison</th>
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##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="-log10(adj p-value)">-log10(adj p-value)</th>
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##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="Mean log2FC">Mean log2FC</th>
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##   <tbody class="gt_table_body">
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">chromosome segregation</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">36.852</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">74</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.983</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">36.170</td>
## <td headers="Count" class="gt_row gt_right gt_striped">65</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.703</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">mitotic cell cycle process</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">36.170</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">96</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.900</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">nuclear chromosome segregation</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">29.184</td>
## <td headers="Count" class="gt_row gt_right gt_striped">52</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.031</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">chromosome organization</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">28.831</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">76</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.837</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">nuclear division</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">27.500</td>
## <td headers="Count" class="gt_row gt_right gt_striped">61</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.946</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">sister chromatid segregation</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">26.900</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">43</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.978</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">organelle fission</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">25.799</td>
## <td headers="Count" class="gt_row gt_right gt_striped">63</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.895</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">DNA-templated DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">25.586</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">43</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.777</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">mitotic sister chromatid segregation</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">23.570</td>
## <td headers="Count" class="gt_row gt_right gt_striped">38</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.047</td></tr>
##   </tbody>
##   
##   
## </table>
## </div>
## 
## $Parasite_Effect_KEGG
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##   <thead>
##     <tr class="gt_heading">
##       <td colspan="5" class="gt_heading gt_title gt_font_normal" style>Top KEGG Pathways - Parasite_Effect</td>
##     </tr>
##     <tr class="gt_heading">
##       <td colspan="5" class="gt_heading gt_subtitle gt_font_normal gt_bottom_border" style>Pathway enrichment (top 10 per contrast)</td>
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##       <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="Treatment Comparison">Treatment Comparison</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="KEGG Pathway">KEGG Pathway</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="-log10(adj p-value)">-log10(adj p-value)</th>
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##   <tbody class="gt_table_body">
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Cell cycle</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">25.694</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">54</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.848</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">20.877</td>
## <td headers="Count" class="gt_row gt_right gt_striped">24</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.671</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Mismatch repair</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">8.846</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">12</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.708</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Homologous recombination</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">7.418</td>
## <td headers="Count" class="gt_row gt_right gt_striped">14</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.756</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Fanconi anemia pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">6.917</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">15</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.918</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">PPAR signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">5.354</td>
## <td headers="Count" class="gt_row gt_right gt_striped">18</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.483</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Nucleotide excision repair</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">5.151</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">14</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.554</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">FoxO signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">4.314</td>
## <td headers="Count" class="gt_row gt_right gt_striped">24</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−0.288</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">p53 signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">4.265</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">16</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">0.420</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Base excision repair</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">3.862</td>
## <td headers="Count" class="gt_row gt_right gt_striped">11</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.612</td></tr>
##   </tbody>
##   
##   
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## </div>
## 
## $Historical_Contingency_GO
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##   <thead>
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##       <td colspan="5" class="gt_heading gt_title gt_font_normal" style>Top GO Terms - Historical_Contingency</td>
##     </tr>
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##       <td colspan="5" class="gt_heading gt_subtitle gt_font_normal gt_bottom_border" style>Biological Process enrichment (top 10 per contrast)</td>
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##       <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="Treatment Comparison">Treatment Comparison</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="GO Term">GO Term</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="-log10(adj p-value)">-log10(adj p-value)</th>
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##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="Mean log2FC">Mean log2FC</th>
##     </tr>
##   </thead>
##   <tbody class="gt_table_body">
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">acrosome reaction</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.215</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">3.216</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left gt_striped">apoptotic signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.215</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.223</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">cell-cell adhesion via plasma-membrane adhesion molecules</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.215</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−3.567</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left gt_striped">egg coat formation</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.215</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">3.216</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">homophilic cell adhesion via plasma membrane adhesion molecules</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.215</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−3.567</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left gt_striped">positive regulation of acrosome reaction</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.215</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">3.216</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">regulation of acrosome reaction</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.215</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">3.216</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left gt_striped">binding of sperm to zona pellucida</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.173</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">3.216</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">cellular modified amino acid biosynthetic process</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.173</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.540</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left gt_striped">heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.173</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−3.993</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">sperm-egg recognition</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.173</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">3.216</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left gt_striped">actomyosin structure organization</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.385</td>
## <td headers="Count" class="gt_row gt_right gt_striped">4</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.032</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">regulation of reactive oxygen species metabolic process</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.385</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.697</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left gt_striped">one-carbon compound transport</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.022</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.215</td></tr>
##   </tbody>
##   
##   
## </table>
## </div>
## 
## $Historical_Contingency_KEGG
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##       <td colspan="5" class="gt_heading gt_title gt_font_normal" style>Top KEGG Pathways - Historical_Contingency</td>
##     </tr>
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##       <td colspan="5" class="gt_heading gt_subtitle gt_font_normal gt_bottom_border" style>Pathway enrichment (top 10 per contrast)</td>
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##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="-log10(adj p-value)">-log10(adj p-value)</th>
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##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Arginine and proline metabolism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.953</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.540</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Cytoskeleton in muscle cells</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.560</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.540</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Drug metabolism - cytochrome P450</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.871</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.293</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Metabolism of xenobiotics by cytochrome P450</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.871</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
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##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Drug metabolism - other enzymes</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.744</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.293</td></tr>
##   </tbody>
##   
##   
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## </div>
## 
## $Recovery_Analysis_GO
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## </style>
##   <table class="gt_table" data-quarto-disable-processing="false" data-quarto-bootstrap="false">
##   <thead>
##     <tr class="gt_heading">
##       <td colspan="5" class="gt_heading gt_title gt_font_normal" style>Top GO Terms - Recovery_Analysis</td>
##     </tr>
##     <tr class="gt_heading">
##       <td colspan="5" class="gt_heading gt_subtitle gt_font_normal gt_bottom_border" style>Biological Process enrichment (top 10 per contrast)</td>
##     </tr>
##     <tr class="gt_col_headings">
##       <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="Treatment Comparison">Treatment Comparison</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="GO Term">GO Term</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="-log10(adj p-value)">-log10(adj p-value)</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="Gene Count">Gene Count</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="Mean log2FC">Mean log2FC</th>
##     </tr>
##   </thead>
##   <tbody class="gt_table_body">
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">defense response</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">8.202</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">13</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.390</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to virus</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">8.202</td>
## <td headers="Count" class="gt_row gt_right gt_striped">8</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.820</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">defense response to other organism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">7.622</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">11</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.700</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to biotic stimulus</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">7.622</td>
## <td headers="Count" class="gt_row gt_right gt_striped">12</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.653</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">response to external biotic stimulus</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">7.622</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">12</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.653</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to other organism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">7.622</td>
## <td headers="Count" class="gt_row gt_right gt_striped">12</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.653</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">defense response to symbiont</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">5.901</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">6</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.735</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">defense response to virus</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">5.901</td>
## <td headers="Count" class="gt_row gt_right gt_striped">6</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.735</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">cytokine-mediated signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.734</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">4</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.223</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">cellular response to cytokine stimulus</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.700</td>
## <td headers="Count" class="gt_row gt_right gt_striped">4</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.223</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">cellular response to chemokine</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.795</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">chemokine-mediated signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.795</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">response to chemokine</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.795</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">granulocyte chemotaxis</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.526</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">neutrophil chemotaxis</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.526</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">granulocyte migration</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.523</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">leukocyte chemotaxis</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.523</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">neutrophil migration</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.523</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">L-phenylalanine catabolic process</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.871</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">L-phenylalanine metabolic process</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.871</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">alpha-amino acid metabolic process</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−1.070</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">amino acid metabolic process</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.070</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">antimicrobial humoral immune response mediated by antimicrobial peptide</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.340</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">arachidonate transport</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.772</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">arachidonic acid secretion</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.772</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">carboxylic acid transport</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−3.378</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">cell chemotaxis</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">cellular response to cytokine stimulus</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">chemotaxis</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">cytokine-mediated signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">endothelial to hematopoietic transition</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.754</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">erythrose 4-phosphate/phosphoenolpyruvate family amino acid catabolic process</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.871</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">erythrose 4-phosphate/phosphoenolpyruvate family amino acid metabolic process</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.871</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">icosanoid secretion</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.772</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">icosanoid transport</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.772</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">inflammatory response</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">leukocyte migration</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">myeloid leukocyte migration</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">organic acid transport</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−3.378</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">organic anion transport</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−3.378</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">polyamine metabolic process</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.730</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">positive regulation of wound healing</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.754</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">regulation of blood coagulation</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.754</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">regulation of hemostasis</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.754</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">regulation of neural retina development</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−3.621</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to cytokine</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">taxis</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">tyrosine metabolic process</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.871</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">cellular response to estrogen stimulus</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">11.573</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−9.231</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to estrogen</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">11.573</td>
## <td headers="Count" class="gt_row gt_right gt_striped">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−9.231</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">response to estradiol</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">11.015</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">6</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−9.270</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to lipid</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">6.552</td>
## <td headers="Count" class="gt_row gt_right gt_striped">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−8.304</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">cellular response to hormone stimulus</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">6.376</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−9.231</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">lipid transport</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">5.844</td>
## <td headers="Count" class="gt_row gt_right gt_striped">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−8.837</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">response to hormone</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">5.844</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−9.231</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to organic cyclic compound</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">5.812</td>
## <td headers="Count" class="gt_row gt_right gt_striped">6</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−9.270</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">lipid localization</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">5.777</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−8.837</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to oxygen-containing compound</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">4.495</td>
## <td headers="Count" class="gt_row gt_right gt_striped">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−8.304</td></tr>
##   </tbody>
##   
##   
## </table>
## </div>
## 
## $Recovery_Analysis_KEGG
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##   <table class="gt_table" data-quarto-disable-processing="false" data-quarto-bootstrap="false">
##   <thead>
##     <tr class="gt_heading">
##       <td colspan="5" class="gt_heading gt_title gt_font_normal" style>Top KEGG Pathways - Recovery_Analysis</td>
##     </tr>
##     <tr class="gt_heading">
##       <td colspan="5" class="gt_heading gt_subtitle gt_font_normal gt_bottom_border" style>Pathway enrichment (top 10 per contrast)</td>
##     </tr>
##     <tr class="gt_col_headings">
##       <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="Treatment Comparison">Treatment Comparison</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="KEGG Pathway">KEGG Pathway</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="-log10(adj p-value)">-log10(adj p-value)</th>
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##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="Mean log2FC">Mean log2FC</th>
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##   </thead>
##   <tbody class="gt_table_body">
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">NOD-like receptor signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">3.914</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">5</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.313</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">RIG-I-like receptor signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">3.914</td>
## <td headers="Count" class="gt_row gt_right gt_striped">4</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.309</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Herpes simplex virus 1 infection</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">3.777</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">5</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−7.243</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Toll-like receptor signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">3.605</td>
## <td headers="Count" class="gt_row gt_right gt_striped">4</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.535</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Apoptosis</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.526</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">3</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.431</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Cytokine-cytokine receptor interaction</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.526</td>
## <td headers="Count" class="gt_row gt_right gt_striped">3</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.422</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Cytosolic DNA-sensing pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.526</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−1.699</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">C-type lectin receptor signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.049</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−3.372</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Linoleic acid metabolism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.262</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.772</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Phenylalanine metabolism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.262</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.871</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Primary bile acid biosynthesis</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.262</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−1.270</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Ubiquinone and other terpenoid-quinone biosynthesis</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.262</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.871</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">alpha-Linolenic acid metabolism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.262</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.772</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Arachidonic acid metabolism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.226</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.772</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Arginine and proline metabolism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.226</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.730</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Cysteine and methionine metabolism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.226</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.871</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Ether lipid metabolism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.226</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.772</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Glutathione metabolism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.226</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.730</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Tyrosine metabolism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.226</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.871</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Glycerolipid metabolism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.877</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.896</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Glycerophospholipid metabolism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.776</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−1.896</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Folate transport and metabolism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.222</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.609</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Protein export</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.222</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−1.277</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">RNA polymerase</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.222</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.415</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">One carbon pool by folate</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.213</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.609</td></tr>
##     <tr><td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Cytosolic DNA-sensing pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.078</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.415</td></tr>
##   </tbody>
##   
##   
## </table>
## </div>
## 
## $Combined_GO
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##   <thead>
##     <tr class="gt_heading">
##       <td colspan="6" class="gt_heading gt_title gt_font_normal" style>Combined GO Terms Summary</td>
##     </tr>
##     <tr class="gt_heading">
##       <td colspan="6" class="gt_heading gt_subtitle gt_font_normal gt_bottom_border" style>Top enriched biological processes across all analyses</td>
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##       <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="Analysis">Analysis</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="Treatment Comparison">Treatment Comparison</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="GO Term">GO Term</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="-log10(adj p-value)">-log10(adj p-value)</th>
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##   <tbody class="gt_table_body">
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">43.746</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">82</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.963</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">mitotic cell cycle process</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">35.875</td>
## <td headers="Count" class="gt_row gt_right gt_striped">114</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.204</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">DNA-templated DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">33.442</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">56</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.020</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">chromosome organization</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">31.704</td>
## <td headers="Count" class="gt_row gt_right gt_striped">94</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.083</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">chromosome segregation</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">31.165</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">79</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.272</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">nuclear division</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">28.063</td>
## <td headers="Count" class="gt_row gt_right gt_striped">72</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.269</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">DNA repair</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">27.219</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">104</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.964</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">DNA damage response</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">27.194</td>
## <td headers="Count" class="gt_row gt_right gt_striped">122</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.901</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">nuclear chromosome segregation</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">25.738</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">56</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.292</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">organelle fission</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">25.633</td>
## <td headers="Count" class="gt_row gt_right gt_striped">74</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.219</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">defense response</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">8.202</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">13</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.390</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to virus</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">8.202</td>
## <td headers="Count" class="gt_row gt_right gt_striped">8</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.820</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">defense response to other organism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">7.622</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">11</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.700</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to biotic stimulus</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">7.622</td>
## <td headers="Count" class="gt_row gt_right gt_striped">12</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.653</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">response to external biotic stimulus</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">7.622</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">12</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.653</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to other organism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">7.622</td>
## <td headers="Count" class="gt_row gt_right gt_striped">12</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.653</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">defense response to symbiont</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">5.901</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">6</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.735</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">defense response to virus</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">5.901</td>
## <td headers="Count" class="gt_row gt_right gt_striped">6</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.735</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">cytokine-mediated signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.734</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">4</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.223</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">cellular response to cytokine stimulus</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.700</td>
## <td headers="Count" class="gt_row gt_right gt_striped">4</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.223</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">36.497</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">85</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.148</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">chromosome segregation</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">32.107</td>
## <td headers="Count" class="gt_row gt_right gt_striped">92</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.423</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">DNA repair</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">31.115</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">129</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.005</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">DNA-templated DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">31.074</td>
## <td headers="Count" class="gt_row gt_right gt_striped">60</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.136</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">DNA damage response</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">30.391</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">151</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.930</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">mitotic cell cycle process</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">30.295</td>
## <td headers="Count" class="gt_row gt_right gt_striped">124</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.368</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">chromosome organization</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">27.626</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">103</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.307</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">nuclear division</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">26.108</td>
## <td headers="Count" class="gt_row gt_right gt_striped">80</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.535</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">nuclear chromosome segregation</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">24.428</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">62</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.532</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">organelle fission</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">23.724</td>
## <td headers="Count" class="gt_row gt_right gt_striped">83</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.440</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">cellular response to chemokine</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.795</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">chemokine-mediated signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.795</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">response to chemokine</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.795</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">granulocyte chemotaxis</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.526</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">neutrophil chemotaxis</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.526</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">granulocyte migration</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.523</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">leukocyte chemotaxis</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.523</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">neutrophil migration</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.523</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">L-phenylalanine catabolic process</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.871</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">L-phenylalanine metabolic process</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.871</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">alpha-amino acid metabolic process</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−1.070</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">amino acid metabolic process</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.070</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">antimicrobial humoral immune response mediated by antimicrobial peptide</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.340</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">arachidonate transport</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.772</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">arachidonic acid secretion</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.772</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">carboxylic acid transport</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−3.378</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">cell chemotaxis</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">cellular response to cytokine stimulus</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">chemotaxis</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">cytokine-mediated signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">endothelial to hematopoietic transition</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.754</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">erythrose 4-phosphate/phosphoenolpyruvate family amino acid catabolic process</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.871</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">erythrose 4-phosphate/phosphoenolpyruvate family amino acid metabolic process</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.871</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">icosanoid secretion</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.772</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">icosanoid transport</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.772</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">inflammatory response</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">leukocyte migration</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">myeloid leukocyte migration</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">organic acid transport</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−3.378</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">organic anion transport</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−3.378</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">polyamine metabolic process</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.730</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">positive regulation of wound healing</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.754</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">regulation of blood coagulation</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.754</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">regulation of hemostasis</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.754</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">regulation of neural retina development</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−3.621</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to cytokine</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">taxis</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">tyrosine metabolic process</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.871</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">41.099</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">88</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.140</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">DNA repair</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">40.741</td>
## <td headers="Count" class="gt_row gt_right gt_striped">140</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.898</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">DNA damage response</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">37.952</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">160</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.848</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">DNA-templated DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">35.898</td>
## <td headers="Count" class="gt_row gt_right gt_striped">63</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.153</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">chromosome segregation</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">33.055</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">91</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.647</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">chromosome organization</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">32.854</td>
## <td headers="Count" class="gt_row gt_right gt_striped">108</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.362</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">mitotic cell cycle process</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">30.759</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">122</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.402</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">nuclear division</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">27.337</td>
## <td headers="Count" class="gt_row gt_right gt_striped">80</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.561</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">organelle fission</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">25.691</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">84</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.425</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">nuclear chromosome segregation</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">25.468</td>
## <td headers="Count" class="gt_row gt_right gt_striped">62</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.739</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">cellular response to estrogen stimulus</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">11.573</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−9.231</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to estrogen</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">11.573</td>
## <td headers="Count" class="gt_row gt_right gt_striped">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−9.231</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">response to estradiol</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">11.015</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">6</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−9.270</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to lipid</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">6.552</td>
## <td headers="Count" class="gt_row gt_right gt_striped">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−8.304</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">cellular response to hormone stimulus</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">6.376</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−9.231</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">lipid transport</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">5.844</td>
## <td headers="Count" class="gt_row gt_right gt_striped">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−8.837</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">response to hormone</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">5.844</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−9.231</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to organic cyclic compound</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">5.812</td>
## <td headers="Count" class="gt_row gt_right gt_striped">6</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−9.270</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">lipid localization</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">5.777</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−8.837</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to oxygen-containing compound</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">4.495</td>
## <td headers="Count" class="gt_row gt_right gt_striped">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−8.304</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">chromosome segregation</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">36.852</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">74</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.983</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">36.170</td>
## <td headers="Count" class="gt_row gt_right gt_striped">65</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.703</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">mitotic cell cycle process</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">36.170</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">96</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.900</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">nuclear chromosome segregation</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">29.184</td>
## <td headers="Count" class="gt_row gt_right gt_striped">52</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.031</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">chromosome organization</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">28.831</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">76</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.837</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">nuclear division</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">27.500</td>
## <td headers="Count" class="gt_row gt_right gt_striped">61</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.946</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">sister chromatid segregation</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">26.900</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">43</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.978</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">organelle fission</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">25.799</td>
## <td headers="Count" class="gt_row gt_right gt_striped">63</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.895</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">DNA-templated DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">25.586</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">43</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.777</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">mitotic sister chromatid segregation</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">23.570</td>
## <td headers="Count" class="gt_row gt_right gt_striped">38</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.047</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Historical_Contingency</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">acrosome reaction</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.215</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">3.216</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Historical_Contingency</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left gt_striped">apoptotic signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.215</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.223</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Historical_Contingency</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">cell-cell adhesion via plasma-membrane adhesion molecules</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.215</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−3.567</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Historical_Contingency</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left gt_striped">egg coat formation</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.215</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">3.216</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Historical_Contingency</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">homophilic cell adhesion via plasma membrane adhesion molecules</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.215</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−3.567</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Historical_Contingency</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left gt_striped">positive regulation of acrosome reaction</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.215</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">3.216</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Historical_Contingency</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">regulation of acrosome reaction</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.215</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">3.216</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Historical_Contingency</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left gt_striped">binding of sperm to zona pellucida</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.173</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">3.216</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Historical_Contingency</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">cellular modified amino acid biosynthetic process</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.173</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.540</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Historical_Contingency</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left gt_striped">heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.173</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−3.993</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Historical_Contingency</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">sperm-egg recognition</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.173</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">3.216</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Historical_Contingency</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left gt_striped">actomyosin structure organization</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.385</td>
## <td headers="Count" class="gt_row gt_right gt_striped">4</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.032</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Historical_Contingency</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">regulation of reactive oxygen species metabolic process</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.385</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.697</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Historical_Contingency</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left gt_striped">one-carbon compound transport</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.022</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.215</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Parasite_Effect</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">chromosome segregation</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">36.852</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">74</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.983</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Parasite_Effect</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">36.170</td>
## <td headers="Count" class="gt_row gt_right gt_striped">65</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.703</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Parasite_Effect</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">mitotic cell cycle process</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">36.170</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">96</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.900</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Parasite_Effect</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">nuclear chromosome segregation</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">29.184</td>
## <td headers="Count" class="gt_row gt_right gt_striped">52</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.031</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Parasite_Effect</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">chromosome organization</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">28.831</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">76</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.837</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Parasite_Effect</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">nuclear division</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">27.500</td>
## <td headers="Count" class="gt_row gt_right gt_striped">61</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.946</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Parasite_Effect</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">sister chromatid segregation</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">26.900</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">43</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.978</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Parasite_Effect</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">organelle fission</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">25.799</td>
## <td headers="Count" class="gt_row gt_right gt_striped">63</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.895</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Parasite_Effect</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">DNA-templated DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">25.586</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">43</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.777</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Parasite_Effect</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">mitotic sister chromatid segregation</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">23.570</td>
## <td headers="Count" class="gt_row gt_right gt_striped">38</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.047</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">defense response</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">8.202</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">13</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.390</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to virus</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">8.202</td>
## <td headers="Count" class="gt_row gt_right gt_striped">8</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.820</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">defense response to other organism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">7.622</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">11</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.700</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to biotic stimulus</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">7.622</td>
## <td headers="Count" class="gt_row gt_right gt_striped">12</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.653</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">response to external biotic stimulus</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">7.622</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">12</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.653</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to other organism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">7.622</td>
## <td headers="Count" class="gt_row gt_right gt_striped">12</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.653</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">defense response to symbiont</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">5.901</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">6</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.735</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">defense response to virus</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">5.901</td>
## <td headers="Count" class="gt_row gt_right gt_striped">6</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.735</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">cytokine-mediated signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.734</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">4</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.223</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">cellular response to cytokine stimulus</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.700</td>
## <td headers="Count" class="gt_row gt_right gt_striped">4</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.223</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">cellular response to chemokine</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.795</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">chemokine-mediated signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.795</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">response to chemokine</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.795</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">granulocyte chemotaxis</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.526</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">neutrophil chemotaxis</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.526</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">granulocyte migration</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.523</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">leukocyte chemotaxis</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.523</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">neutrophil migration</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.523</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">L-phenylalanine catabolic process</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.871</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">L-phenylalanine metabolic process</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.871</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">alpha-amino acid metabolic process</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−1.070</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">amino acid metabolic process</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.070</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">antimicrobial humoral immune response mediated by antimicrobial peptide</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.340</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">arachidonate transport</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.772</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">arachidonic acid secretion</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.772</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">carboxylic acid transport</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−3.378</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">cell chemotaxis</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">cellular response to cytokine stimulus</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">chemotaxis</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">cytokine-mediated signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">endothelial to hematopoietic transition</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.754</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">erythrose 4-phosphate/phosphoenolpyruvate family amino acid catabolic process</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.871</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">erythrose 4-phosphate/phosphoenolpyruvate family amino acid metabolic process</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.871</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">icosanoid secretion</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.772</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">icosanoid transport</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.772</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">inflammatory response</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">leukocyte migration</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">myeloid leukocyte migration</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">organic acid transport</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−3.378</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">organic anion transport</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−3.378</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">polyamine metabolic process</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.730</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">positive regulation of wound healing</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.754</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">regulation of blood coagulation</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.754</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">regulation of hemostasis</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.754</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">regulation of neural retina development</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−3.621</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to cytokine</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.906</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">taxis</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.448</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.906</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">tyrosine metabolic process</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.448</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.871</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">cellular response to estrogen stimulus</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">11.573</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−9.231</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to estrogen</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">11.573</td>
## <td headers="Count" class="gt_row gt_right gt_striped">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−9.231</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">response to estradiol</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">11.015</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">6</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−9.270</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to lipid</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">6.552</td>
## <td headers="Count" class="gt_row gt_right gt_striped">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−8.304</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">cellular response to hormone stimulus</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">6.376</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−9.231</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">lipid transport</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">5.844</td>
## <td headers="Count" class="gt_row gt_right gt_striped">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−8.837</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">response to hormone</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">5.844</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−9.231</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to organic cyclic compound</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">5.812</td>
## <td headers="Count" class="gt_row gt_right gt_striped">6</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−9.270</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">lipid localization</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">5.777</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−8.837</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">response to oxygen-containing compound</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">4.495</td>
## <td headers="Count" class="gt_row gt_right gt_striped">7</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−8.304</td></tr>
##   </tbody>
##   
##   
## </table>
## </div>
## 
## $Combined_KEGG
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##   <thead>
##     <tr class="gt_heading">
##       <td colspan="6" class="gt_heading gt_title gt_font_normal" style>Combined KEGG Pathways Summary</td>
##     </tr>
##     <tr class="gt_heading">
##       <td colspan="6" class="gt_heading gt_subtitle gt_font_normal gt_bottom_border" style>Top enriched pathways across all analyses</td>
##     </tr>
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##       <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="Analysis">Analysis</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="Treatment Comparison">Treatment Comparison</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="KEGG Pathway">KEGG Pathway</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="-log10(adj p-value)">-log10(adj p-value)</th>
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##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" style="font-weight: bold;" scope="col" id="Mean log2FC">Mean log2FC</th>
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##   </thead>
##   <tbody class="gt_table_body">
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">26.277</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">30</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.993</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Cell cycle</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">26.007</td>
## <td headers="Count" class="gt_row gt_right gt_striped">63</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.012</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Mismatch repair</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">14.304</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">17</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.748</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Homologous recombination</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">14.148</td>
## <td headers="Count" class="gt_row gt_right gt_striped">22</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.889</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Fanconi anemia pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">9.354</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">20</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.078</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">PPAR signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">8.502</td>
## <td headers="Count" class="gt_row gt_right gt_striped">26</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.268</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Base excision repair</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">6.112</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">16</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.792</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">FoxO signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">5.928</td>
## <td headers="Count" class="gt_row gt_right gt_striped">33</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−0.250</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Nucleotide excision repair</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">5.625</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">17</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.775</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Apoptosis</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">5.402</td>
## <td headers="Count" class="gt_row gt_right gt_striped">34</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">0.474</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">p53 signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">5.402</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">21</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">0.495</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">NOD-like receptor signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">3.914</td>
## <td headers="Count" class="gt_row gt_right gt_striped">5</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.313</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">RIG-I-like receptor signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">3.914</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">4</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.309</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Herpes simplex virus 1 infection</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">3.777</td>
## <td headers="Count" class="gt_row gt_right gt_striped">5</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−7.243</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Toll-like receptor signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">3.605</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">4</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.535</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Apoptosis</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.526</td>
## <td headers="Count" class="gt_row gt_right gt_striped">3</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.431</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Cytokine-cytokine receptor interaction</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.526</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">3</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−1.422</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Cytosolic DNA-sensing pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.526</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.699</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">C-type lectin receptor signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.049</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−3.372</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Cell cycle</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">26.135</td>
## <td headers="Count" class="gt_row gt_right gt_striped">73</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.270</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">22.544</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">30</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.015</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Mismatch repair</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">15.314</td>
## <td headers="Count" class="gt_row gt_right gt_striped">19</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.882</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Homologous recombination</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">13.636</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">24</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.036</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Fanconi anemia pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">12.606</td>
## <td headers="Count" class="gt_row gt_right gt_striped">26</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.121</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Drug metabolism - other enzymes</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">7.972</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">32</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−0.879</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">PPAR signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">7.673</td>
## <td headers="Count" class="gt_row gt_right gt_striped">29</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.527</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Base excision repair</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">7.507</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">20</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.782</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Drug metabolism - cytochrome P450</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">6.812</td>
## <td headers="Count" class="gt_row gt_right gt_striped">24</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.723</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Retinol metabolism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">5.872</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">26</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−1.511</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Linoleic acid metabolism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.262</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.772</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Phenylalanine metabolism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.262</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.871</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Primary bile acid biosynthesis</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.262</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.270</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Ubiquinone and other terpenoid-quinone biosynthesis</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.262</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.871</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">alpha-Linolenic acid metabolism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.262</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.772</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Arachidonic acid metabolism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.226</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.772</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Arginine and proline metabolism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.226</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.730</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Cysteine and methionine metabolism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.226</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.871</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Ether lipid metabolism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.226</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.772</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Glutathione metabolism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.226</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.730</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Tyrosine metabolism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.226</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.871</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">28.698</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">34</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.996</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Cell cycle</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">27.177</td>
## <td headers="Count" class="gt_row gt_right gt_striped">75</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.317</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Homologous recombination</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">14.390</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">25</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.161</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Mismatch repair</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">13.479</td>
## <td headers="Count" class="gt_row gt_right gt_striped">18</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.039</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Fanconi anemia pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">13.309</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">27</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.180</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Base excision repair</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">12.892</td>
## <td headers="Count" class="gt_row gt_right gt_striped">26</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.610</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">PPAR signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">12.527</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">36</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−1.403</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Proteasome</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">8.327</td>
## <td headers="Count" class="gt_row gt_right gt_striped">23</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.305</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Nucleotide excision repair</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">7.055</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">22</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.758</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Apoptosis</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">6.211</td>
## <td headers="Count" class="gt_row gt_right gt_striped">44</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">0.543</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">FoxO signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">6.211</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">41</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">0.010</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Glycerolipid metabolism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.877</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.896</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Glycerophospholipid metabolism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.776</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−1.896</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Folate transport and metabolism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.222</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.609</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Protein export</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.222</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−1.277</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">RNA polymerase</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.222</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.415</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">One carbon pool by folate</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.213</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.609</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Cytosolic DNA-sensing pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.078</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.415</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Cell cycle</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">25.694</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">54</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.848</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">20.877</td>
## <td headers="Count" class="gt_row gt_right gt_striped">24</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.671</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Mismatch repair</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">8.846</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">12</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.708</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Homologous recombination</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">7.418</td>
## <td headers="Count" class="gt_row gt_right gt_striped">14</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.756</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Fanconi anemia pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">6.917</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">15</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.918</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">PPAR signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">5.354</td>
## <td headers="Count" class="gt_row gt_right gt_striped">18</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.483</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Nucleotide excision repair</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">5.151</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">14</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.554</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">FoxO signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">4.314</td>
## <td headers="Count" class="gt_row gt_right gt_striped">24</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−0.288</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">p53 signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">4.265</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">16</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">0.420</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">All_Treatments</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Base excision repair</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">3.862</td>
## <td headers="Count" class="gt_row gt_right gt_striped">11</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.612</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Historical_Contingency</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Arginine and proline metabolism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.953</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.540</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Historical_Contingency</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Cytoskeleton in muscle cells</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.560</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.540</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Historical_Contingency</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Drug metabolism - cytochrome P450</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.871</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.293</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Historical_Contingency</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Metabolism of xenobiotics by cytochrome P450</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.871</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.293</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Historical_Contingency</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P+ vs A- T- P+</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Drug metabolism - other enzymes</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.744</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.293</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Parasite_Effect</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Cell cycle</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">25.694</td>
## <td headers="Count" class="gt_row gt_right gt_striped">54</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.848</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Parasite_Effect</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">DNA replication</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">20.877</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">24</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.671</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Parasite_Effect</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Mismatch repair</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">8.846</td>
## <td headers="Count" class="gt_row gt_right gt_striped">12</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.708</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Parasite_Effect</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Homologous recombination</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">7.418</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">14</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.756</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Parasite_Effect</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Fanconi anemia pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">6.917</td>
## <td headers="Count" class="gt_row gt_right gt_striped">15</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.918</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Parasite_Effect</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">PPAR signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">5.354</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">18</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−1.483</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Parasite_Effect</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Nucleotide excision repair</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">5.151</td>
## <td headers="Count" class="gt_row gt_right gt_striped">14</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">1.554</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Parasite_Effect</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">FoxO signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">4.314</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">24</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−0.288</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Parasite_Effect</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">p53 signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">4.265</td>
## <td headers="Count" class="gt_row gt_right gt_striped">16</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">0.420</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Parasite_Effect</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T- P+ vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Base excision repair</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">3.862</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">11</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">1.612</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">NOD-like receptor signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">3.914</td>
## <td headers="Count" class="gt_row gt_right gt_striped">5</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.313</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">RIG-I-like receptor signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">3.914</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">4</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.309</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Herpes simplex virus 1 infection</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">3.777</td>
## <td headers="Count" class="gt_row gt_right gt_striped">5</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−7.243</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Toll-like receptor signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">3.605</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">4</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.535</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Apoptosis</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.526</td>
## <td headers="Count" class="gt_row gt_right gt_striped">3</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.431</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Cytokine-cytokine receptor interaction</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.526</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">3</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−1.422</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Cytosolic DNA-sensing pathway</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.526</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.699</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">C-type lectin receptor signaling pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.049</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−3.372</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Linoleic acid metabolism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.262</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.772</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Phenylalanine metabolism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.262</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.871</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Primary bile acid biosynthesis</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.262</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.270</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Ubiquinone and other terpenoid-quinone biosynthesis</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.262</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.871</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">alpha-Linolenic acid metabolism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.262</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.772</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Arachidonic acid metabolism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.226</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.772</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Arginine and proline metabolism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.226</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">2.730</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Cysteine and methionine metabolism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.226</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−4.871</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Ether lipid metabolism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.226</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.772</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Glutathione metabolism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.226</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">2.730</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A+ T- P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Tyrosine metabolism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.226</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−4.871</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Glycerolipid metabolism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.877</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−1.896</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Glycerophospholipid metabolism</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.776</td>
## <td headers="Count" class="gt_row gt_right gt_striped">2</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.896</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Folate transport and metabolism</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.222</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−2.609</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">Protein export</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.222</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−1.277</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">RNA polymerase</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.222</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−1.415</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left gt_striped" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left gt_striped">One carbon pool by folate</td>
## <td headers="log_padj" class="gt_row gt_right gt_striped">1.213</td>
## <td headers="Count" class="gt_row gt_right gt_striped">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right gt_striped">−2.609</td></tr>
##     <tr><td headers="analysis" class="gt_row gt_left" style="background-color: #E8F4FD;">Recovery_Analysis</td>
## <td headers="contrast" class="gt_row gt_left" style="background-color: #E8F4FD;">A- T+ P- vs A- T- P-</td>
## <td headers="Description" class="gt_row gt_left" style="background-color: #F7F7F7;">Cytosolic DNA-sensing pathway</td>
## <td headers="log_padj" class="gt_row gt_right" style="background-color: #F7F7F7;">1.078</td>
## <td headers="Count" class="gt_row gt_right" style="background-color: #F7F7F7;">1</td>
## <td headers="mean_log2FC" class="gt_row gt_right" style="background-color: #F7F7F7;">−1.415</td></tr>
##   </tbody>
##   
##   
## </table>
## </div>

Export Results

Export Significant Genes in Long Format (DESeq2-style)

Session Info

sessionInfo()

## R version 4.3.3 (2024-02-29)
## Platform: x86_64-apple-darwin20 (64-bit)
## Running under: macOS 15.3
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib 
## LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## time zone: America/Los_Angeles
## tzcode source: internal
## 
## attached base packages:
## [1] grid      stats4    stats     graphics  grDevices utils     datasets 
## [8] methods   base     
## 
## other attached packages:
##  [1] furrr_0.3.1                 future_1.33.2              
##  [3] org.Dr.eg.db_3.18.0         AnnotationDbi_1.64.1       
##  [5] clusterProfiler_4.10.1      coin_1.4-3                 
##  [7] rstatix_0.7.2               multcomp_1.4-25            
##  [9] TH.data_1.1-2               MASS_7.3-60.0.1            
## [11] survival_3.6-4              mvtnorm_1.2-5              
## [13] emmeans_1.10.1              car_3.1-2                  
## [15] carData_3.0-5               broom_1.0.6                
## [17] gt_0.10.1                   BiocParallel_1.36.0        
## [19] gridExtra_2.3               VennDiagram_1.7.3          
## [21] futile.logger_1.4.3         lubridate_1.9.3            
## [23] forcats_1.0.0               stringr_1.5.1              
## [25] dplyr_1.1.4                 purrr_1.0.2                
## [27] readr_2.1.5                 tidyr_1.3.1                
## [29] tibble_3.2.1                tidyverse_2.0.0            
## [31] ggrepel_0.9.5               RColorBrewer_1.1-3         
## [33] pheatmap_1.0.12             ggplot2_3.5.1              
## [35] DESeq2_1.42.1               SummarizedExperiment_1.32.0
## [37] Biobase_2.62.0              MatrixGenerics_1.14.0      
## [39] matrixStats_1.3.0           GenomicRanges_1.54.1       
## [41] GenomeInfoDb_1.38.8         IRanges_2.36.0             
## [43] S4Vectors_0.40.2            BiocGenerics_0.48.1        
## 
## loaded via a namespace (and not attached):
##   [1] splines_4.3.3           bitops_1.0-7            ggplotify_0.1.2        
##   [4] cellranger_1.1.0        polyclip_1.10-6         lifecycle_1.0.4        
##   [7] rprojroot_2.0.4         globals_0.16.3          lattice_0.22-6         
##  [10] backports_1.5.0         magrittr_2.0.3          sass_0.4.9             
##  [13] rmarkdown_2.26          jquerylib_0.1.4         yaml_2.3.8             
##  [16] cowplot_1.1.3           DBI_1.2.3               abind_1.4-5            
##  [19] zlibbioc_1.48.2         ggraph_2.2.1            RCurl_1.98-1.14        
##  [22] yulab.utils_0.2.0       tweenr_2.0.3            sandwich_3.1-0         
##  [25] GenomeInfoDbData_1.2.11 enrichplot_1.22.0       listenv_0.9.1          
##  [28] tidytree_0.4.6          parallelly_1.37.1       codetools_0.2-20       
##  [31] DelayedArray_0.28.0     DOSE_3.28.2             xml2_1.3.6             
##  [34] ggforce_0.4.2           tidyselect_1.2.1        aplot_0.2.3            
##  [37] farver_2.1.2            viridis_0.6.5           jsonlite_1.8.8         
##  [40] tidygraph_1.3.1         tools_4.3.3             treeio_1.26.0          
##  [43] Rcpp_1.0.12             glue_1.7.0              SparseArray_1.2.4      
##  [46] xfun_0.43               here_1.0.1              qvalue_2.34.0          
##  [49] withr_3.0.0             formatR_1.14            fastmap_1.2.0          
##  [52] fansi_1.0.6             digest_0.6.35           timechange_0.3.0       
##  [55] R6_2.5.1                gridGraphics_0.5-1      estimability_1.5       
##  [58] colorspace_2.1-0        GO.db_3.18.0            RSQLite_2.3.6          
##  [61] utf8_1.2.4              generics_0.1.3          data.table_1.15.4      
##  [64] graphlayouts_1.1.1      httr_1.4.7              S4Arrays_1.2.1         
##  [67] scatterpie_0.2.4        pkgconfig_2.0.3         gtable_0.3.5           
##  [70] modeltools_0.2-23       blob_1.2.4              XVector_0.42.0         
##  [73] shadowtext_0.1.4        htmltools_0.5.8.1       fgsea_1.28.0           
##  [76] scales_1.3.0            png_0.1-8               ggfun_0.1.5            
##  [79] knitr_1.45              lambda.r_1.2.4          rstudioapi_0.16.0      
##  [82] tzdb_0.4.0              reshape2_1.4.4          coda_0.19-4.1          
##  [85] nlme_3.1-164            cachem_1.1.0            zoo_1.8-12             
##  [88] parallel_4.3.3          HDO.db_0.99.1           libcoin_1.0-10         
##  [91] pillar_1.9.0            vctrs_0.6.5             xtable_1.8-4           
##  [94] evaluate_0.23           cli_3.6.2               locfit_1.5-9.9         
##  [97] compiler_4.3.3          futile.options_1.0.1    rlang_1.1.4            
## [100] crayon_1.5.2            labeling_0.4.3          plyr_1.8.9             
## [103] fs_1.6.4                stringi_1.8.4           viridisLite_0.4.2      
## [106] munsell_0.5.1           Biostrings_2.70.3       lazyeval_0.2.2         
## [109] GOSemSim_2.28.1         Matrix_1.6-5            hms_1.1.3              
## [112] patchwork_1.2.0         bit64_4.0.5             KEGGREST_1.42.0        
## [115] highr_0.10              igraph_2.0.3            memoise_2.0.1          
## [118] bslib_0.7.0             ggtree_3.13.0.001       fastmatch_1.1-4        
## [121] bit_4.0.5               readxl_1.4.3            gson_0.1.0             
## [124] ape_5.8